Atomic force microscopy (AFM) and infrared (IR) spectroscopy have been combined in a single instrument (AFM-IR) capable of producing sub-micrometer spatial resolution IR spectra and absorption images. This new capability enables the spectroscopic characterization of micro-domain-forming polymers at levels not previously possible. Films of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) were solution cast on ZnSe prisms, followed by melting and annealing to generate crystalline microdomains of different sizes. A tunable IR laser generating pulses of the order of 10 ns was used for excitation of the sample films. Short duration thermomechanical waves, due to infrared absorption and resulting thermal expansion, were studied by monitoring the resulting excitation of the contact resonance modes of the AFM cantilever. Dramatic differences in the room-temperature IR spectra are observed in the 1200–1300 cm−1 range as a function of position on a spatial scale of less than one micrometer. This spectral region is particularly sensitive to the polymer backbone conformation. Such dramatic spectral differences have also been observed previously in bulk IR measurements, but only by comparing room-temperature spectra with ones collected at higher temperatures. Less dramatic, but significant, AFM-IR spectral differences are observed in the carbonyl stretching region around 1720 cm−1 as a function of location on the sample. Two overlapping, but relatively sharp, carbonyl bands are observed near 1720 cm−1 in more crystalline regions of the polymer, while a broader carbonyl stretching band appears centered at 1740 cm−1 in the more amorphous regions. Using this spectral region, it is possible to monitor the development of polymer crystalline structures at varying distances from a nucleation site, where the site was generated by bringing a heated AFM tip close to a specific location to locally anneal the sample.