After various cookie operations I'm left with some pretty ugly geo; open faces and intersecting polys. Is there anyway to procedurally cleanup such geo so I'm able to perform further cuts succesfully?

I can group all the bad geo by colour but am not sure what I could do next. I don't want to rebuild the geo using iso surfacing as I believe I would lose the inside groups I created which I will later require for texturing.

Any suggestions would be hugely appreciated.

Thanks
S