Much like the limit switches, the FLA kit didn't come with any clamping system so it's up to you to create your own. I spent a few months sticking parts on some old plywood with double-stick tape before I finally realized how I wanted to do it. In the end I settled on a hybrid horizontal/vertical approach:
Since I use my machine for a variety of purposes, I wanted a surface that would be modular. I also wanted to be able to resurface it for perfect alignment and to remove any scratches or *oops* that might come up. To accomplish this I used a single large sheet of 3/4" mdf for the base with additional strips of 3/4" mdf on top alternating with aluminum t-tracks. The tracks were purchased from Orange Aluminum and they work very well for this purpose. They're a little smaller and seem a little less durable than other products on the market, but I challenge you to come anywhere close for the price. Since the tracks are 1/2" high and the mdf is 3/4" this this gives me 1/4" to work with for resurfacing. So far I've only used a couple hundredths of it (and no *oops* yet).
So far I've used 2 different approaches to clamp material to the tracks:
Other custom jigs can be made as long as they have 1/4" bolts. One of the first that I'm planning on making is a pcb engraving jig with more frequent resurfacing and registration points for double-sided boards.
Vertical clamping seems to be a bit more rare in the DIY CNC machine world. In fact, I couldn't find a single FLA-100 that had one. Some of the other designs I saw for other machines called for a slot opening in the center of the table, but I didn't have much space below the table. I wanted to be able to use it on large workpieces, so instead I decided to flip the gantry to allow the router to reach beyond the edge of the table. This sacrificed a few inches of X travel on the table, but I felt this was worth it for the additional functionality. The frame rails stick out a little less than an inch and I wanted longer pieces to be able to clear the frame in the -Y direction, so I decided to make the table side of the clamp an inch thick. The bottom layer is 1/4" mdf next to a 1.5"x1.5"x0.25" aluminum angle for a vertical stop at the +Y end of the table. On top of that I put another layer of 3/4" MDF.
All of the pieces were aligned so that they were parallel with their respective axes. The moving part of the clamp was made from a piece of 1530 extrusion with a piece of 3/4" MDF bolted to the face. This made it less prone to marring wood and also provided clearance for the aluminum vertical stop. Clamping pressure is provided by a pair of F clamps that are bolted to the frame using 80/20 gussets. The clamps are oriented vertically so that a long workpiece (like a table leg) can protrude past the frame. This configuration allows for cutting proper dovetails, tenons, and mortises with ease. It also allows me to cut nice round handles for my 4th axis to grab onto. One of the greatest features of the vertical axis is that the location of the workpiece is known in both X (the table end) and Y (the vertical stop). This means I can just clamp the piece, run the auto-zero macro using my touch plate and then run the program.