A sample mapping system includes a sample chuck including absolute reference marks, an imaging metrology tool to capture sets of alignment images at locations associated with sample marks on a sample on the sample chuck, and a controller. A particular set of alignment images at a particular location may include at least one alignment image associated with a particular sample mark and at least one alignment image associated with a particular portion of the absolute reference marks within a field of view of the imaging metrology tool visible through the sample. The controller may determine absolute coordinates of the sample marks based on the sets of alignment images. Determining the absolute coordinates of the particular sample mark may include determining the absolute coordinates of the particular sample mark based on a position of the particular sample mark relative to the particular portion of the absolute reference marks.