If the Done button is missing when you’re using the Subtract tool, there can be several reasons:
The body you want to subtract has already been subtracted, so there's no intersection between the bodies.
If there is no Done button after selecting at least two bodies, look for two things:
- Double-check if there’s a clear intersection between the bodies.
- Check whether the Subtract tool has already been applied before. In certain settings, the Subtract tool will keep the bodies after applying the tool. In these scenarios, there is nothing to subtract. If you encounter this issue, please check if that was the first time the tool is applied with the intersecting bodies.
You can specify the settings for how the Subtract tool manages the original bodies and the new bodies created from subtraction: 
- All (Default): Select this option if you want to keep the original bodies and the subtracted body. If you started with two bodies, you'll end up with three:
- Modified Bodies: Select this option if you want to keep the original of the body from which you subtracted. In this example, the cube:
- Removed Bodies: Select this option if you want to keep the body that was subtracted, so you can use the tool body later.
- None: Select this option if you don't want to keep the original bodies at all. Only the subtracted target body will remain.
The subtraction would result in bodies with zero thickness.
Zero thickness means that a geometry has no thickness. In Shapr3D, a subtraction is considered an error if it results in geometry with zero thickness. For example:
Subtracting the red body from the green one would result in details with zero thickness at the lowest point, where the blue circle is placed. This is why the Done button is missing, and a line appears along the lowest area of the red cylinder.
If you subtract the red cylinder from the green one, the thickness would be zero along that line—this is an invalid body for Shapr3D, a solid body modeling software. To make the subtraction possible, move the red cylinder upwards, or the green one lower to get a clear intersection.