Is the move widget on your shape in Blender partially or completely missing?
In the above image, notice that the move widget on the selected shape has only one arrow instead of 3 allowing movement only in that direction. Look to the right of the selected shape in the Location section of the panel, and notice that the y and z locations are locked. That keeps you from accidentally moving it in the 3d View. If you clock on the locks, those directions will be unlocked and the other two arrows on the move widget will return
Sometimes the SimuSEM extension will lock one or more axes in location and/or rotation on a particular shape by default, if it is likely that it should not be moved. For instance, the location of the substrate layers are locked in all 3 axes by default. However, if you want to move a shape in a direction that is locked, you can either unlock it or type in a new location in that panel. Or if you don't want to accidentally transform an object, you can lock the location, rotation and/or scale of any axis manually.
Why can't I select any objects?
If you are trying to select an object, but you can't, one likely cause is that you are in Edit Mode. You need to be in Object mode to select an object. Edit mode will allow you to select a part of an object, which is sometimes useful in SimuSEM. Whenever you are asked to select a vertex, edge or face of an object, you are in Edit Mode in Blender. SimuSEM always has a Cancel button next to buttons that switch to Edit Mode, such as Choose a Pixel or Cursor to Face buttons. However, you can always switch back to Object mode by click in the field circled in the above figure. You can not add new shape in Edit Mode.