Deleting invisible parts

Hi! I want to delete invisible (cropped and overlapped) parts of a .pdf file I created using Inkscape. I tried almost everything (flatten, re-print, optimize...) unsuccesfully. The only solution I found is using the option Remove Hidden Data, but my file looses vectors and the final quality is quite poor. 
What I want is to obtain a final .pdf file with only the objects that are "visible", because when oppening it again on Inkscape, Gimp or similar, everyone can use the tool Release Cropped objects and 'see' images that should not be there.
I would appreciate some help on this! 
Thank you in advance!