Any idea which bit of software is at fault? Or is it something I’m not doing? I’ve created a test object in FreeCAD, using the Pocket function to cut holes. I can see that Slic3r gets some of the info for them, but they’re filled not empty. FreeCAD 1.4 and Slic3r 1.0.0.RC2.
Checklist questions: What does it look like from slic3r if you look somewhere in the middle of the z-height? Are there voids with a skin over them or is it solid? (Also, does downloading a later version help any?)
@paul_wallich both tell me I’m running the latest version.
@An_R_key so you’re suggesting I add Cura to my work flow? I’m wondering if it would be simpler to switch to simplify3d and do both slicing and printing in the one app.
It seems that you have exported 2 models at the same time: the one with holes and the one without them. Make sure only one is selected before exporting to stl.
@Mark_MARKSE_Emery
According to http://slic3r.org, current is 1.21 or 1.17stable. Might make a difference, might not.
Try slicing in cura. Then play with the fix horrible settings under expert settings. I find that depending on how you cut in freecad it sometimes looks like its cut but for some reason its not. What you can try is exporting the stl. Then open a new freecad project import the stl. Create a mesh from it, refine the model and then convert to solid. Then export that and see what it looks like in your slicer
Do you have “support material” turned on in Slic3r and not in Cura?
Thanks all! The Slic3r check for updates isn’t working then. I’ll do a fresh download and retest. Maybe FreeCAD is exporting both the original pad and cut one? Thanks again 
@NathanielStenzel thanks for the idea but I don’t think it’s a support material issue, it was doing a consistent fill pattern from start to finish, so maybe the duplicate objects in export is more likely. If the pockets were seen properly it would have drawn outline around the hole.
Haha, of all the bugs! One in the code that checks if you’re up to date has to be the worst. Downloading slic3r-mswin-x64-1-1-7-stable.zip.
It turns out it was the idiot driving the software. @Juan_Gonzalez_Gomez was spot on. I must have selected everything, which would have been the first pad and each pocketed varieant.
One is glad to be of service 
@Juan_Gonzalez_Gomez
You’ve been watching Bicentennial Man haven’t you? One of my faves, Mr. Martin.
@Theophilus_Stark All right film, just 2 hours and 45 minutes too long.
A tip about working in FreeCAD: after an operation, if an object is hidden automatically by the system, there’s a reason for it. It means it was superseded by a new object/feature. Leave it hidden unless you need to edit it. Then hide it back again once done. When exporting to CAD or mesh formats, only select what’s visible in the 3D view, not the whole tree.
That was the problem. I’d done an export that had no data in it, Slic3r would bomb out. I then went from one extreme to the other by typing Ctrl-A which selects all objects, hidden and visible. I should have been more selective. Lesson well and truly learnt
I’m surprised FreeCAD let you export with no data. Since v0.14.3700 it requires an object to be selected for File --> Export to work and advises the user about it (it didn’t in the past, which obviously led to confusion for users). If you can reproduce this would be worth reporting.
Me too. On other occasions I have had it warn that nothing was selected.
