First of all what version and build number of BobCAD are you using.
If I am understanding this correctly the areas currently shown with toolpaths in them you want them to not have toolpaths, is it the main shape you want to pocket and leave the inner shapes uncut ?
If yes then chain select the outer shape for a pocket and then select the inner shapes as islands
Better if you can upload the BobCAD file (In a Zip file), makes for easier understanding.
Regards
Rob