Filtering options

I am unable to have it reconstruct the regions that I have selected, it reverts to the original auto-alignment.  The “Filter Tool” is a reference to something that is absent, the box, and advanced tools are difficult to apply.  I got it to work once and don’t recall what made it work.  I thought that I started a new model.  But when I do it just reverts to what I had an hour before.  Once I have the object highlighted or what I want deleted highlighted, what do I do to get it to run and produce the model?