Smallest dot/dot indent for Prusa MK3S using PLA
There is no direct limit on the size of a hole in XY-plane (that means: oriented so that the hole is visible from above).

The movement accuracy of MK3S (and most other modern 3D printers) is about 0.01 mm. So theoretically you could move around a circle that has diameter of the (default) 0.4 mm extrusion width + 0.01 mm, and get a 0.01 mm hole in the middle of the circle.

In practice, the hole size will be limited by the repeatability of the extrusion width. If in the above example the extrusion width happens to be 0.41 mm instead, there would be no hole remaining.

On a well calibrated printer, 1/4th of the nozzle size should be manageable, i.e. for MK3S you should be able to get 0.1 mm holes quite reliably.