In FDM, there will always be a variation between what you have in the slicer and the actual diameter of a 3D printed hole. Horizontal holes, for example, are notorious for not being perfectly round, while vertical holes often come out smaller than intended.
A horizontal hole faces the problem that its face is composed of multiple layers with varying degrees of overhang. As such, some sections of the curve might not come out perfectly round.
The reason a vertical hole is often smaller than expected is that the compressing force of the nozzle squishes the perimeter lines next to the hole. If these lines turn out wider than intended, the hole will be narrower than intended.
The narrower the hole is designed, the more likely these phenomena are to cause problems.
Solution #1: Change the shape of the hole.
Instead of designing a circular hole, go for a teardrop shape, which your FDM printer can easily handle.
With horizontal holes, this will give you a margin of error on droopage. Tear-dropping limits overhangs to 45 degrees and makes large holes printable. With vertical holes, you’re allowed some slack with fitted parts.
This solution works especially well with functional parts, where the appearance of the hole is not as important. If, however, you’re against it, or the design simply cannot accommodate it, create a thin support membrane to hold up the top of the hole.
Solution #2: Design small and drill after.
The amount of variation will often depend on the printer in question, the size of the hole, the slicing software, and the material. Getting an accurate diameter may require you to perform several test prints.
However, if you want a much higher accuracy, or if your hole has a tight tolerance, print the hole undersized and drill it to the correct diameter.
Solution #3: Design a wider hole.
MachineDesign recommends that you design your hole with a diameter that is greater than 1 mm (0.04”) if you want it to retain a circular shape.
With vertical holes, if you know the amount by which the diameters are reduced, you can simply design the hole to be that much wider. Of course, this may require some testing…
(Note that MachineDesign is using what Xometry offers for FDM parts.)