The piece holders we use at Yale are top-surface referenced. In other words, the top of the substrate is pushed onto the correct focus plane. Residual dirt or resist on the back of the substrate will not change the position of the front surface. It is much easier to mount pieces in this holder, as long as the substrate is at least 2mm wider than the widow width. See next slide for a list of window sizes. If you have a substrate that does not fit any of these, it is easy to have the machine shop build a new one.
This top-referenced holder was first developed at Cornell University (for a JEOL system) and later used at IBM and many other laboratories.