Dynamic IR radiation power control, beam steering and focus adjustment for use in a nanoscale IR spectroscopy system based on an Atomic Force Microscope. During illumination with a beam from an IR source, an AFM probe tip interaction with a sample due to local IR sample absorption is monitored. The power of the illumination at the sample is dynamically decreased to minimize sample overheating in locations/wavelengths where absorption is high and increased in locations/wavelengths where absorption is low to maintain signal to noise. Beam alignment and focus optimization as a function of wavelength are automatically performed.