Before widening any hole, make sure it's okay to do so. Some holes shouldn't be widened beyond a certain point because they will hold a self-tapping screw that has no nut on the other end. If you widen such a hole too much, you may have to re-print the part, or figure out some other way of dealing with it.
If a hole is to be widened until a given screw will slide freely through it, generally the quickest way is to use a drill bit.
But drilling can be hazardous. Drilling safely requires a vise or similar to hold the work piece, but many of the printed parts don't fit well in a vise. If you simply hold the work piece in your hand, the bit might grab it and spin it around and generally create mayhem, so don't do this.
Fortunately, the plastic material used here is soft enough so that a safer alternative can be used.
Install your drill bit on your drill, but don't power up the drill. Simply screw your plastic part onto the bit, by hand, just as if you were threading a nut onto a screw:
When the part is fully onto the bit, twirl it around a few times with your finger (don't hurt your finger). Then pull it off, while slowly turning it in the same direction.
This makes a clean hole, is often quicker and more accurate than using a rotating bit, and is definitely safer.
Check for small bits of plastic left clinging to the edges of the hole. If you find them protruding above a flat surface, a sharp woodworking chisel, applied lightly, will remove them.
This method also works with thin pieces of wood, such as the base of the hot end.
It doesn't work as well with really large parts, or really large holes, but it should suffice for all of the holes you might need to widen while building a Bukobot.
Remove the drill bit from the drill when not in use. Don't leave the drill lying around on the workbench with the bit extending over the edge.
If you need to slightly widen a hole in a metal part, such as in the flat metal parts in the Bukobot, you can use a hand reamer:
But try just threading the screw through the hole before resorting to the reamer. The screw is steel, the hole is aluminum, so if it's a slightly tight fit you shouldn't have any trouble getting it in. Only use the reamer if excessive force is needed to get the screw through. So far, nobody has reported needing a reamer for Bukobot parts.