To subtract geometry objects from other geometry objects to make a set difference, in the Geometry toolbar, from the 
Boolean and Partitions (

) menu, select 
Difference (

). You can also right-click the 
Geometry node to add this node from the 
Boolean and Partitions submenu. Then enter the properties of the difference operation using the following section:
 
    Activate the Objects to add list by clicking the 
Active button to toggle between turning ON 

 and OFF 

 selections. When set to ON, select the objects that you want to add in the 
Graphics window. If the geometry sequence includes user-defined selections above the 
Difference node, choose 
Manual to select objects, or choose one of the selection nodes from the list next to 
Objects to add.
 
    Activate the Objects to subtract list by clicking the 
Active button to toggle ON and OFF. When set to ON, select the objects that you want to subtract in the 
Graphics window. If the geometry sequence includes user-defined selections above the 
Difference node, choose 
Manual to select objects, or choose one of the selection nodes from the list next to 
Objects to subtract.
 
    Click the Swap Objects to Add and Objects to Subtract button (

) to swap the objects in the two lists.
 
    Select the Keep objects to add to use the geometry objects to add for further geometry operations. Select the 
Keep objects to subtract to use the geometry objects to subtract for further geometry operations.
 
    Create a geometry object without interior boundaries by clearing the Keep interior boundaries check box. This can be useful to simplify a geometry where the interior boundaries do not separate domains with different physics nodes or materials, for example.
 
    You can change the settings for the Repair tolerance list if you experience problems with the difference operation. Geometric entities that have a distance less than the repair tolerance are merged.
 
    Select the Resulting objects selection check box to create predefined selections (for all levels — objects, domains, boundaries, edges, and points — that are applicable) in subsequent nodes in the geometry sequence. To also make all or one of the types of resulting entities (domains, boundaries, edges, and points) that the resulting objects consist of available as selections in all applicable selection lists (in physics and materials settings, for example), choose an option from the 
Show in physics (
Show in instances if in a geometry part; 
Show in 3D in a plane geometry under a work plane in a 3D component) list: 
All levels, 
Domain selection, 
Boundary selection, 
Edge selection, or 
Point selection. The default is 
Domain selection, which is suitable for use with materials and physics defined in domains. For use with a boundary condition, for example, choose 
Boundary selection. These selections do not appear as separate selection nodes in the model tree. Select 
Off to not make any selection available outside of the geometry sequence. From the 
Color list, choose a color for highlighting the resulting objects selection. See 
Selection Colors.
 
    
    From the Construction geometry list choose 
On to make the resulting objects available only in the feature’s geometry sequence. The default option 
Inherit means that the resulting objects become construction geometry if all input objects are construction geometry. Choose 
Off to never output construction geometry objects. For more information see 
Construction Geometry.