The basic entity that some operations work with is the "selection". This is basically a set of shapes of instances on which an operation should be applied. A selection can be established by either clicking on a element in "Select" mode or by dragging a selection rectangle. When the mouse is released, all elements inside the selection rectangle are selected.
The selection set can be modified by adding elements (press the Shift button in addition to selecting elements), by removing elements (press Ctrl in addition) or by toggling the selecting (press Shift and Ctrl in addition: remove already selected ones and add new ones).