DRI

• Draw the assembly of the parts in the form of solids. Blocks, Surface, Mesh and flat drawings will be ignored. Use any of the layers.
• Switch the default layer to "Holes".  If you do not have such a layer - create it. Layer settings do not matter - the main thing that corresponded to the layer name.  Or use DRI with option "HoleLayer".
• Draw holes in the form of cylinders or any other solids. One hole can penetrate as much as necessary details. This ensures concentricity. Optimize and negotiate the location of fasteners at this stage. For standard fasteners useful blocks containing fasteners and holes-body.
• Call command Drill (DRI). Command will use the preselected object if possible. If not selected, command will require select solids and will show options: Gap, SaveHoles|DeleteHoles, and HoleLayer.
  • Gap - option to configure the gap between details. If you set gap more than zero programs will increase (inflate, swell) hole-solids before subtraction.
  • SaveHoles|DeleteHoles - You can choose to delete hole-solids at end of work or not delete.  Solid in block never deleted.
  • HoleLayer - enter layer name.
• If layer Holes do not exist you will see a dialog window with layer list. You must click on the layer with hole-solids. Only the selected object layer is on the list.
• After selecting all solids, wait for the end of the command. If a thousand details, the better to prepare tea. Working time grows geometrically with the number of holes. But it is still much faster than doing a separate command _Subtract every hole.
• At the end of its work, the program will show how to make a hole.

If was allowed to record the solid history, it will be automatically disabled. I strongly recommend disabling recording solid history from the beginning of modeling (System variable SolidHist = 0). 

Follow the messages on the console. There may be error messages.

GAP

• Call the command Gap.
• Select Gap option if you need to change the gap (clearance) between the parts. By default, the gap is zero, and the command works like a normal subtraction of solid.
• Select the first group of solids of which will be subtracted. You can select these items in advance of the call command. Objects can be a lot, they do not stick together in a single entity. Blocks and other objects will be discarded.
• Select the second group of objects. These objects will be used as the subtracted. There already may select blocks. All subtrahend items are always stored in the drawing.
• The program will show the progress bar and starts to subtract all of the intersecting body.
• At the end of the program will show how many subtractions made.

The installer that ran when you downloaded this app/plug-in from Autodesk App Store will start installing the app/plug-in. OR, simply double-click the downloaded installer to install the app/plugin. You may need to restart the Autodesk product to activate the app/plug-in. To uninstall this plug-in, exit the Autodesk product if you are currently running it, simply rerun the installer, and select the "Uninstall" button. OR, click Control Panel > Programs > Programs and Features (Windows 7/8/8.1/10) and uninstall as you would any other application from your system.