I cut a lot of small pieces out of sheet and there are a lot of fixture/clamps involved. I set the z-height low so it goes fast. I then edit the g-code to make sure if it's passing over a clamp or hold-down I raise the cutter an extra 1/2 inch. Is there a way of marking where the clamps are and then having the g-code automatically fly high over those areas? As things stand I'm using a g-code editor but it's a pay product (not to mention it's tedious)... any features that might help?
I don't think that there is a program that will do what you want. Maybe one of the paid programs can do it but I wouldn't be surprised if that program cost a few thousands.
Programs like Fusion360 can do that BUT you have to draw all the clamps as part of your fixture first and remember to tell it to be fixture aware. SketchUcam does know how to 'stay down' for layers within a cut but has no idea how to jump over fixtures since it is not 3D aware. Also be aware that the optimization will affect the cut sequence which means that the motion between cuts is not always the same, a simple edit can change the group/object order which may then put a clamp in the way that was previously not in the way. Maybe there is a way to reduce the height of your clamps, or even eliminate them. Have you heard of the tape+ca glue method? This allows you to mount flat sheet without clamps yet remove the cut parts easily, much more easily than double sided tape. and it even works for large aluminum parts in the 'real mill'