Mister 3d,
I think you have already figured this out , but to be sure, in the ribbon in the "Geomagic Design" screen there is a button marked Boolean . Read the instructions on the use of this.
To Create a Boolean Design Feature
1. Open the blank part.
2. From the Geometry Transform group in the Part Modeling tab, select Feature > Boolean > Subtract (or Unite, or Intersect). The Insert Part/Subassembly dialog box will be displayed.
3. Highlight the part or assembly you wish to use for the tool, then click OK. The part workspace window transforms into the Design Boolean Editor window. Click in the Editor workspace to place the tool. Click Finish when you have the number of copies desired.
a. You can repeat steps 2 and 3 to add as many parts or assemblies as required.
4. Constrain the tool(s) to the blank using the assembly constraints available in the Boolean editor workspace.
5. Click the Commit icon to complete the Boolean feature. The window transforms back into the blank part workspace, and the Boolean feature will be listed as a feature in the design explorer.
Note: If a part or assembly in the tool is hidden in the dedicated assembly, it will not participate in the Design Boolean feature until it is unhidden.
B.E.
You are judged not by what you know, but by what you can do.