This answer assumes you're working in the Part Design workbench.
So you want to adjust the starting height of a pad or pocket. There are two ways I can think of to do this easily.
Adjust the Z attachment value of the sketch to lower the sketch below the surface.
Use the "two dimensions" option in the pad/pocket operation and set the second value ...
I am sorry to tell you that SketchUp is not a good software for printable 3D designs due to its exporting feature not properly reducing complexity. It creates unnecessary faces and vertices inside of items on a regular basis, which in the slicer creates artifacts.
To make a SketchUp created file well printable, a huge amount of careful re-engineering in a ...
SketchUp does not always create STLs in ways that are closed, watertight manifolds - a block with a bore is, if created as a block first and then bored out, actually 2 surfaces if made with SketchUp:
a cylinder with its normals facing inside and no top and bottom
a block that has 2 holes in opposite surfaces
The two surfaces are not ...
I would like a better answer involving automatic alignment, but this was my solution.
Make the object a single component.
Make sure the guide points are accurately located.
Cut and copy the first component to the origin.
Copy the component to the guide points.
What also worked better was to break the grouping of components into building blocks that could ...
I have been down that road with FreeCAD and STL files and never ever succeeded. I actually use Prusa Slic3r whenever I need to edit STL files such as resize, cut or split and object.
That said, FreeCAD is extremely powerful when you learn how to use it. It took me several months to get a good workflow with part design and the ability to write scripts/tools ...
There are a number of steps to importing an STL file into FreeCAD and being able to use it.
This page discusses this in detail, but to summarize:
Import the STL
In the Part workbench, use Create shape from mesh.
Use the Advanced utility and select Solid from shell.
Now I will tell you from personal experience, you still may not be able to what you want to ...
Stls may not properly import as solids. This is likely what is happening in your case. Stl format is ultimately just a bunch of triangles without a proper definition of a solid. The boolean Difference found faces to attach to the circle so it used them. The trouble is, there were even more faces at the same location (not uncommon).
You could manually ...