Hey Mike! I actually had to google some Romulan ships to figure out what you were looking at.
Not too knowledgeable on the ships....
Anyway, without seeing were you are working...Applying the putty, try cutting a small thin piece of flat stock (plastic, metal shim or even balsa). The little bit of flex in the applicator allows the putty to go on easier. Too ridgid and it scrapes off, too flexy it clumps on. Try layers too. Apply, then sand, add some more, and so forth. If it real tiny, some thick super glue applied with a piece of wire to fill in the area works nice and can be sanded.
Sanding... Have you tried wrapping or gluing a piece of sandpaper to a small flat piece of styrene, wood or small enough object to get into the crease and not hit another part? Even and old #11 blade. Super glue and have at it. You could try a flex-file. I cut old ones down to odd shapes to try and get where no man has gone before (sorry, couldn't resist) . Small flat needle file?
Side note: Sorry to hear about your catastrophic fuselage placement on the X-wing.. Post a pick of what you got. I found the aint nuttin' that can't be fixed. Trust me, graduated Summa Cum Laude of Dr. Big Finger's school of "oh crap, I broke it again 101". I think almost everybody here can pitch an idea out to ya!
Hang in there! 8)