<p>I am using an M3D printer and loaded an STL design with holes in the middle:</p>

<p><a href="https://i.stack.imgur.com/UMD0V.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/UMD0V.jpg" alt="Screenshot of STL design with holes in the middle"></a></p>

<p>However, the output is an object without holes (so I stopped the printing): </p>

<p><a href="https://i.stack.imgur.com/RrlBC.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/RrlBC.jpg" alt="Photo of the first few layers of actual print, without holes"></a></p>

<p>What can be done to be able to print with holes?</p>

Case 1:
There may be an issue with the precision of the print nozzle, not being able to fully articulate the hole. That is to say, the printer is trying to print it with holes, but the material is filling in that area.
Try increasing the size of the hole. Granted, it is not an exact process but there may be an inner hole diameter that winds up mimicking the diameter you're looking for after the material extrudes.
This case could be rejected by nature of the printer depositing straight lines through the center diameter of the cylinder's base.
Case 2:
There may be some discrepancy between the file's appearance and the file's information.
If you downloaded the file from somewhere like ThingiVerse, try designing the part yourself if possible. If you designed it yourself, overwrite the file with a second version.
Case 3:
If downloaded, verify that the center hole is extruded though the entire thickness of the part. It may be that it's extruded most of the way through and there is a sealed bottom layer.