Subtracting .STL

In the past I thought I had used the subtract function to subtract a .stl file from a object I created in the same project and I was able to edit the resulting object like a normal shapr object. I don’t seem to be able to do that now? In the example the bottom box is the stl file and the top is the result from subtracting the stl from a cube I drew and extruded in the same project. Before the subtract function I’m able to edit the cube normally after the subtract I can’t.

How can I do this?