Photolysis of caged compounds is a powerful tool for studying subcellular physiological functions. Here we describe protocols for the alignment and calibration of a focal uncaging system. We also report procedures for convenient quantitative calibration of uncaging. Using these methods, we can achieve submicron lateral resolution of photolysis and probe biological function in spines, the smallest signaling compartments of neurons. Initially, the entire alignment procedure takes 4-6 h to perform; periodic fine-tuning of the system takes 1-2 h.