This protocol describes the technique Cell Labeling via Photobleaching (CLaP) for adding fluorescent tags to individual cells in a microscopy field based on their shape, position, behavior, or any other visual feature. The procedure tethers biotin molecules to the cell membrane using a focused laser beam. Biotinylated cells are subsequently tagged by adding fluorescent streptavidin conjugates to the culture medium. The method can be used for tracking cells, and it can be combined with flow cytometry or microfluidics-based single-cell capture for genomic or other biochemical analysis. The whole procedure typically takes one hour, plus one extra minute for each tagged cell.