A novel spectroscopy technique to enable the rapid characterization of discrete mid-infrared integrated photonic waveguides is demonstrated. The technique utilizes lithography patterned polymer blocks that absorb light strongly within the molecular fingerprint region. These act as integrated waveguide detectors when combined with an atomic force microscope that measures the photothermal expansion when infrared light is guided to the block. As a proof of concept, the technique is used to experimentally characterize propagation loss and grating coupler response of Ge-on-Si waveguides at wavelengths from 6 to 10 µm. In addition, when the microscope is operated in scanning mode at fixed wavelength, the guided mode exiting the output facet is imaged with a lateral resolution better than 500 nm i.e. below the diffraction limit. The characterization technique can be applied to any mid-infrared waveguide platform and can provide non-destructive in-situ testing of discrete waveguide components.