A method of and system for inspecting multi-layer reticles. The method includes: selecting a multi-layer reticle having an array of cells arranged in R rows and C columns; defining a full inspection region that includes all cells of the array of cells; and when R is equal to one (or is greater than two) and C is greater than two (or is equal to one) and a cell of the array of cells is a dummy cell in a first or last position of a row (or of a column) of the array of cells, then reducing the full inspection region to generate a shrunken inspection region that does not include the dummy cell, and then inspecting the shrunken inspection region for defects. If the dummy cell is between two non-dummy cells, then the dummy cell is a copy of one of the non-dummy cells, but is not inspected.