This is normal, expected, and common in FFF printing. I don't know how Prusa slicer gets around this issue but I suspect they have a parameter (on by default?) like this one in Cura: hole horizontal expansion
I typically get all my vertical holes about 0.4mm too small. Regardless if they are 25mm in diameter or 2mm in diameter.
The problem is that PLA sticks to itself as it prints, like snot or mucus. As it prints the inner wall it is stretched like a liquid rubber band (it's tight because the PLA also shrinks as it cools in the first milliseconds out of the nozzle). This pulls inward and makes vertical holes smaller than desired.
The best solution by far is to just fix it in CAD. Note that the outer diameter can shrink also but not as much as the rest of the part supports that outer wall from shrinking.
All manufacturing techniques (milling, FFF, SLA, injection molding) require that you fudge things like this in CAD. Some people who do injection molding don't know this as the "factory" takes care of that step for you.
I am having exactly the same problem, I am printing a housing for an electric motor. It is essentially a 30x30x45mm block with a cylinder hole with a diameter of 25mm. The print has exactly the correct outer dimensions but the inner cylinder comes out as 24.3mm. The STL file, upon inspection indeed shows 25mm diameter, so it is a slicing or printer settings problem.
I have noticed this as well with other cutouts for panel meters, when I measure the size and use that in whatever 3D modeling package, the printed cutout is too small en I have to experimentally adjust until it fits.
I do not understand whether this is a cura of printer settings feature. A friend who is printing the same STL files with PrusaSlicer and Prusa does not suffer from this feature, the models come out as per the dimensions in the STL file.
I have not been able to fix it to date and appreciate insights from people who may have seen this before and know how to fix.
Best regards, Jeroen
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