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

Screenshot of STL design with holes in the middle

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

Photo of the first few layers of actual print, without holes

What can be done to be able to print with holes?

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    $\begingroup$ Have you tried letting it print a few more layers? It is very common that printers use the few first layers to create a raft, which will make the model adhere better to the bed. $\endgroup$ – Tormod Haugene Dec 4 '16 at 22:14
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    $\begingroup$ You're right its a raft $\endgroup$ – xybrek Dec 5 '16 at 9:17
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    $\begingroup$ @TormodHaugene - You should turn your comment into an answer, as it appears to be the correct solution :-) $\endgroup$ – Greenonline Dec 5 '16 at 9:26
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    $\begingroup$ @Greenonline, done. :-) $\endgroup$ – Tormod Haugene Dec 5 '16 at 10:37
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Have you tried letting it print a few more layers? It is very common that printers use the first few layers to create a raft, which will make the model adhere better to the bed.

I believe this illustration from Simplify3D displays this well:

raft vs skirt vs brim

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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.

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