A method and tool for conducting NIR overlay metrology is disclosed. Such methods involve generating a filtered illumination beam including NIR radiation and directing that illumination beam onto an overlay target to produce an optical signal that is detected and used to generate overlay metrology measurements. The method is particularly suited to substrate applications having layers of opaque material that are transmissive in the NIR range (e.g., amorphous carbon) and where NIR imaging is used to obtain overlay measurements. A tool implementation includes a means for generating a filtered illumination beam extending into the NIR range and a detector for receiving NIR signal from an NIR illuminated target and a computer for processing the signal data to obtain overlay metrology measurements.