Needle punching system

Im currently doing research in my university under microbiology department looking for someone who has knowledge in cell biology and labview software, i need some solutions to some of my problems which im facing in research., The Puncher system is developed to isolate single cells. This is achieved by punching out bottoms of the microwells and collecting it in a container of choice. The Microwells have a diameter of 80µm and the needle that has to punch out the bottoms has a diameter of 70µm. Therefore the alignment of these two parts is very critical (+/- 5µm). In the current design of the Puncher system this has been addressed by using encoder controlled stages and a laser alignment unit to measure the position of the needle. Never the less this does not yet result in a perfect alignment every time, so it would be nice if someone can provide me an idea of how to solve it.