<p>I want to make a project involving many small dots indents and I would like to know how I can calculate the smallest dot hole the Prusa i3 MK3S can extrude around on a layer using PLA. In other words, if I printer a mesh with circle shaped holes, how would I know the minimum diameter of the holes. Is it simply the same as the layer resolution (0.35&nbsp;mm), filament size (1.75&nbsp;mm), or is it something else?</p>

That depends on the ability how fast you get filament to stick to the build plate and whether the filament is loaded in the extruder. It also matters which size of nozzle you are using. The filament diameter has no influence other than smaller filament width (e.g. 1.75 mm) requires more length to extrude with respect to thicker filament (e.g 2.85 or 3.0 mm), and is therefore more precise to lay down (on the other side is the deviation on the filament diameter, i.e. manufacturing tolerance, larger than for thicker filament...).
If it does not stick you need more length, also, if the filament is not preloaded enough, the nozzle chamber needs to be filled first. Note that the printing of several small circles is a challenge, see e.g.
"How do I get circles on small interior holes to adhere to the bed?"
.