This operation use the concept of "primary" and "secondary" selection. The primary selection contains all shapes that are selected in the first step. The secondary selection contains all shapes that are selected in additional steps using the "Shift" modifier key.
The object alignment function allows aligning of all objects in the secondary selection to the objects in the primary selection (i.e. objects in the primary selection define the reference points but are not moved). An "object" can be a shape or an instance of a cell. Cell instances are referred to by their bounding box which can be either computed from the visible layers alone or from all layers.
Alignment can be specified differently in horizontal and vertical direction. Horizontal alignment can be "none" (no change), "left" (align left sides), "center" (align centers) or "right" (align right sides). Vertical alignment can be "none", "bottom", "center" or "top".
The alignment function can be found in the "Selection" submenu of the "Edit" menu. A dialog will open which allows specification of the alignment mode and bounding box computation mode for cell instances.