Methods and apparatus for performing chemical spectroscopy on samples from the scale of nanometers to millimeters or more with a multifunctional platform combining analytical and imaging techniques including atomic force microscopy, infrared spectroscopy, confocal microscopy, Raman spectroscopy and mass spectrometry. For infrared spectroscopy, a sample is illuminated with infrared light and the resulting sample distortion is read out with either a focused UV/visible light beam and/or AFM tip. Using the AFM tip or the UV/visible light beam it is possible to measure the IR absorption characteristics of a sample with spatial resolution ranging from around 1 μm or less to the nanometer scale. The combination of both techniques provides a rapid and large area survey scan with the UV/visible light and a high resolution measurement with the AFM tip. The methods and apparatus also include the ability to analyze light reflected/scattered from the sample via a Raman spectrometer for complementary analysis by Raman spectroscopy. Using a UV/vis source or IR source at higher intensity it is possible to thermally desorb material from a sample for analysis by mass spectrometry. The AFM tip can also be heated to desorb material for mass spec analysis at even higher spatial resolution.