I use a variety of methods depending on the part(s) but generally most part go straight in after cleaning. With screws I like to hammer the burrs back in to place then give the heads a polish in the lathe. It's surprising how old chewed-up screws can be made to look like new with very little effort.
Yes, I use a (fine) file to follow the curves of the head, after that I polish (grain) it with grade 800.
If the thread looks a little damaged or corroded, I cut the thread with a thread cutter.
Damaged "hard to get" nut's are candidates for the milling machine (a one day session once a year because I don't have one my self at home). Big corroded bolts and heavy corroded important bolts and nuts are wet blasted before the sink process.
Having dismantled over 30 engines last year (CB450's and CB72's) I have a box of 25 kilo's of fasteners hardware alone, all ready to get the same treatment, but that's work for the long (next) winter evenings. It's a lot of work, checking bolt by bolt, nut by nut.
The preparations are the most important step in the sink process.