Masked Aligners



Algae can hold up to 60% of its weight in oil and can mature in just hours. Algae could be a great new source of renewable energy.


Inside the pocket of virtually every person in the U.S. is a Microelectro Mechanical System, or MEMS device. Any guesses? It’s your phone! Inside cell phones are tiny components made using microtechnology. Other uses of microtechnology can be seen almost everywhere including computers, car sensors, hearing aids, GPS, etc. Chances are you utilize mircrotechnology on a daily basis and don’t even realize it. One branch of MEMS that has grown significantly in recent years is microfluidics.  Microfluidics are widely used in the medical and bio-medical fields. One of the current developments is to be able to conduct multiple tests with a single drop of blood with a testing chip no larger than a quarter. Another application is to sort cells, such as algae, for renewable biofuel technologies.

Why sort algae cells you ask? Some types of algae hold relatively large amounts of oil. If this oil is harvested, it can be used as a renewable source of energy that yields significantly more oil per acre that most current biofuel sources. Before the cells can be processed, they need to be sorted based on how much oil is stored in each cell. To sort the algae, channels not much larger than the width of a cell need to be made for the sorted algae to flow through. In order to make channels this small, photo-lithography and other MEMS technologies are incorporated by “stacking” multiple layers on top of each other. These layers need to be aligned accurately for proper flow and overall function of the sorting process; that is where the aligner comes in.  Alignments made with a microscope and the human hand are extremely difficult to make with an accuracy less than 100 microns, barely larger than the size of a human hair. The goal of the EZ-Aligner 2013, is to align multiple substrate layers with an accuracy of 25 microns.

What is MEMS you ask?

MEMS (microelectromechanical systems) is engineering focused on studying the behaviors of various phenomena on the micro scale. Typical MEMS devices are built on sizes ranging from 20-100 microns; pretty small when you consider that the size of a human hair is between 50-70 microns. MEMS technology can be found almost everywhere in daily life, from the accelerometers in your car that detect collisions, to the microprocessors in your phone. Although MEMS research focuses on micro versions of virtually any engineering field, one that has grown substantially in recent years is in the area of Bio-MEMS, which focuses on combining micro-technology with biology, particularly in the medical field. A subset of Bio-MEMS is microfluidics, this subset deals with studying and controlling the behavior of fluids constrained to the micro scale. One of the larger scope goals of microfluidics applied in the medical field, is to achieve a similar effect of the increased capabilities of computers, even though they continue to get smaller in size; only for microfluidics, the goal is to minimize the size of a testing lab to something smaller than a business card. An example of a microfluidic chip that could be used for such a task is shown below in Figure 1, this chip could be used to sort and analyze different types of fluids and perform separate analysis on each one. This could greatly reduce the amount of equipment needed in medical testing labs, and the amounts of the sample required to do the tests with.

Figure 1: Example microfluidic device that could be used to sort and analyze fluids, like blood for example, that could greatly reduce the size of test equipment in medical labs.

In order to build devices like the one shown above, each separate fluid (shown as a different color) needs to have an individual layer so as not to interfere with the flow of another layer. Failure to do this could cause inaccurate results due to contamination if used in medical testing applications. Yet, for the overall function of the chip to work, each layer still needs to be aligned on top of the previous one very accurately so that each fluid flows to the proper location for whatever test needs to be conducted. Building each layer is not as simple as adding another layer of material and shaping it to the desired orientation. For MEMS processes, building a chip consists of iterations of layering substrate materials, patterning each layer, and developing or etching the pattern to get the desired shapes in each layer. An example of how a simple microfluidic channel is made is shown below in Figure 2.

Figure 2: A process flow of how a simple microfluidic channel is made using a copper (grey) substrate, FR-4 photoresist (dark blue), silicone (light blue), and glass (green). The end result is rectangular microfluidic channel that is only 20 microns tall and approximately 100 microns wide.

A unique aspect to building these microfluidic devices is that the patterning and developing steps of these processes are often done by uncommon means. For example, the patterning process shown in Figure 2 is actually done using an ultraviolet lamp because the photoresist chemically reacts when exposed to UV light to form a more rigid and robust structure that won’t wash away during the developing step. The developing and/or etching processes can be done in liquid rinses, similar to developing a photograph, or as in several MEMS processes, plasma etching is used to etch away hard materials like metals. The types of structures and devices that can be created using MEMS processes and technology are infinite, and as microtechnology research continues to grow and improve, the applications for MEMS will certainly lead to a very interesting future.



The EZ-aligner was built in order to incorporate a higher degree of precision into the universities research. The research lab currently does the micro alignments by hand which gives them a significant amount of human error in their alignment. This error translates directly to their data affecting the research results in a negative manner. Commercial aligners, which the research lab would need, can cost upwards of 100,000 dollars. A compromise was made between the research lab’s need to eliminate human error and the amount of money it was willing to spend in order to achieve that goal. The EZ-aligners increase in accuracy will be high enough to allow the research lab to obtain better test results while still saving the university a substantial amount of money. The figures below illustrate differences between the EZ-aligner and a commerical aligner.

Fig. 1: Commercial Aligner (Approximately $120,000)


Fig. 2: Masked Aligner’s Micro Aligner (approximately $1500)

Dr. Geiger, the team sponsor, has been doing manual alignments by hand for his research in microfluidics. The most accurate alignment that he has been able to do was within 250 microns. In most sciences this would be an acceptable tolerance, but in the study of microtechnology 250 microns is quite large. This tolerance needed to be dropped down to at least 25 microns, which could only be achieved through a mechanical device. The Masked Aligners team has done just that.



The EZ-aligner is able to move in all the directions required in order to achieve an accurate alignment between two substrates which initially start parallel to each other. The directions include left/right and forwards/backwards (X and Y), a change in height (Z), and theta (rotation), as well as four screws which suspend the entire stage above the base plate in order to allow for leveling prior to the alignment. All these directions of movement are done on the micron scale through the use of micrometers included in the stage. The fine movements of the stage are easy to see with the aid of a digital microscope. Combining all of this mechanical precision equipment results in small amounts of human error.

Fig. 1: Photo of the EZ-Aligner showing the height change (Z), the screws, and the micrometer which controls the right/left and forward/backwards (X and Y) movements.

Once everything is set up, our aligner makes aligning two substrates easy and effective. First, a baseline alignment is done with your eyes and hands, then placed in the EZ-Aligner so the user can look through the microscope and find the alignment structure on the substrates. Second, the user uses the micrometers to adjust the stage so both alignment structures are aligned by alternating between the two structures. Third, once alignment is complete, the substrates are then moved to the exposure systems for the final steps of alignment. Figure two shows the final alignment after exposure.

The finished substrate with the herring bone structure emphasized.

Fig. 2:  The finished substrate after alignment and exposure.  The circle emphasizes the herring bone structure inside the channel.



To make sure our design was on the right track halfway through the design process, we perfomed what was called a Proof of Concept.  This was a small experiment using part of our design.  We chose to make sure the vacuum plate we designed was in working order.  First we machined our top vacuum plate to our designed spec.  We then attached the plate to the tubes connected to the vacuum pump and placed a substrate on the plate.  As we expected the plate held the substrate in place even when turned upside-down.  This confirmed that our top plate design worked and we could move forward with the rest of the design.  This also showed a couple faults with our design of the plate.  With the PDMS substrate placed on the vacuum plate, the PDMS bowed enough to make the alignment impossible.  This showed us we needed an additional top plate made specifically for the PDMS substrate.



In order to test the accuracy of the aligner, multiple dual-layer exposures were done with dry photoresist onto the copper substrate. The masks contained a vernier scale in order to measure the exact difference in the alignment. A vernier scale is a small moveable scale that allows the user to measure more accurately than a stationary measuring instrument. Unfortunately, the scale was too small for the resolution the photoresist could provide. The measurements were then taken from the software of the microscope.

Cross shaped alignemnt structure currently not aligned with the underlying substrate

Alignment marks from the mask and underlying substrate are nearly aligned.

Herring bones aligned to within 30 micron of the channel.


The alignment structures, in the shapes of crosses, are located on two opposite corners of each mask. The herring bones need to be aligned exactly in the channel from thefirst exposure. The herring bones should be aligned inside the channel by aligning these two crosses on the mask and the previously exposed structures. If the crosses are aligned, then the herring bones are aligned.


As you can see from the pictures on the above, the herring bone structure is aligned within the flow channel. However, there is a small misalignment of about 25 microns, most likely due to a minor human error in the theta orientation.





From Left to Right: Joanne Terranova, Kyle Kingery, Brian Lord, Matt Koerner, Holly Cheek

Holly Cheek (Team Leader)

Holly is graduating with her Mechanical Engineering degree from the University of Nevada, Reno in mid May 2013. She started her college career in an Elementary Education major, at which time she met a math professor who opened the world of engineering to her. She then decided to pursue a Mechanical Engineering degree, because of her love of math and tinkering. Holly is a well organized person, pays attention to details, and enjoys being in a leadership role; she quickly volunteered for the Team Leader position once her team, the Masked Aligners, was formed. She is looking forward to her next steps in life working for an engineering company.

Kyle Kingery

Kyle is graduating with his Mechanical Engineering degree from the University of Nevada, Reno in mid May 2013. Kyle went into Mechancial Engineering because he found it more interesting than Civil Engineering.

Matthew Koerner

 Matt is graduating with his Mechanical Engineering degree from the University of Nevada, Reno in mid May 2013. Originally his dream was to build bridges, however once experiencing Civil Engineering classes and Mechanical Engineering classes, he quickly realized that Mechanical courses were much more along the lines of his interest than civil courses. His understanding of tools and innovation in his racing career led him to be more mechanical inclined. He started racing bicycles at the age of 12, motocross at 15, and karts at 19. He will continue to race once his degree is complete and hopes to work in the automotive industry and a Mechanical Engineer.

Joanne Terranova

Joanne was born and raised in Reno, NV. She plans on graduating in May 2013 with a B.S in Mechanical Engineering with a minor in Mathematics. While completing this rigorous coursework, she played collegiate soccer for the University of Nevada for four years from 2008-2011. She is currently coaching youth soccer for Legacy Football Club and plans on starting her career in engineering this summer.

Brian Lord

Brian is graduating with his Mechanical Engineering degree from the University of Nevada, Reno in December of 2013.