We have developed a low-cost micro-diffuse reflectance infrared Fourier transform spectroscopic (micro-DRIFTS) setup for measuring the reflectance of small area diffuse samples. The system performance is characterized and then demonstrated on small area vertically aligned carbon nanotube (VACNT) samples. We find that our system can measure samples with a spatial resolution of approximately 140 µm with sensitivities of 10s of ppm in the 2 µm - 18 µm spectral window. Our uncertainty budget is presented along with how our measured reflectance can be equated to directional-hemispherical reflectance.