I left the original blender file in case the STL doesn't carry over the needed information for modifiers (sorry, I never tested it and was too excited to upload my first model here). In there you'll find an object named Screw_Hole which you can modify to match your needs. The CounterSunk object is… well the countersunk part around the 2 screws, feel free to edit it. 

When you are done, make sure you click apply to all the modifiers as shown in the screenshots and DELETE ALL THE EXTRA FACES left behind after you applied the modifiers (I know there is probably a way to do the booleans better, I just haven't figured out how to do it).

BROKEN EDGES

If when you export you end up with broken edges, add the weld modifier. Check the fix blender file I added with the modifier added (I also Joined all the objects and deleted all the unneeded ones to make it simple). After that, re export the STL and if you're finding it weird that the object is too small, remember to set the multiplier when exporting to 1000 as shown in the last screenshot.