3D printed holes might be smaller than designed or not very accurate. It is useful to drill over the holes to make them fit the screws or prepare them for cutting a thread.
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Get a 2.5 mm drill bit. Check the drill with a caliper to make sure it is the correct size. 2.5 mm is the recommended hole diameter for cutting a M3 thread. 
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Drill the holes - 
(Option 1) Using drill press: - 
Attach the drill bit into the chuck of the drill press. Make sure that the drill bit is centered. 
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Clamp your 3D printed piece into the vice. 
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Place the vice under the drill. 
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Make sure that the drill bit can go far enough to drill through the part. 
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Raise the drill press plate if necessary. 
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Drill through the holes of the part. 
 
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(Option 2) Using cordless drill: - 
Attach the drill bit into the chuck of a cordless drill. 
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Hold the piece with your hand. You can hold it flat on the edge of the table. 
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Drill the holes. 
 
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Cut a thread into the holes. - 
(Option 1) By hand: - 
Get a M3 tap (will be given by instructor). 
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Attach the tap to the tap wrench. 
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Center the tap to the hole. 
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Start turning the tap into the hole clockwise. 
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Try to keep the tap straight with the hole. 
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Tap through the hole. 
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Bring the tap out by turning it counter-clockwise. 
 
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(Option 2) With cordless drill: - 
Attach M3 tap into the chuck of the cordless drill. 
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Set cordless drill clutch to the lowest torque setting (increase the torque setting if the lowest is too weak). Low torque setting helps to prevent destroying the thread by over-torquing it. 
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Set cordless drill speed to 1 (the lowest speed) for better speed control. 
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Make sure that the drill rotates clockwise. 
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Clamp the piece into a vice or hold it flat on the table by hand. 
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Try to keep the tap straight with the hole. 
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Tap through the hole. 
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Bring the tap out by setting the drill to rotate counter-clockwise. 
 
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