We report a method for removing unwanted contributions to fluorescence signals from dyes absorbed in polydimethylsiloxane (PDMS) using fluorescence lifetime imaging microscopy (FLIM). By analysing experimental fluorescence decays using a bi-exponential decay model, we are able to discriminate between emission originating from dye molecules in free solution and those absorbed within the PDMS substrate. Simple image processing allows the unwanted background signal to be removed and thus enables a more accurate assessment of temperature. The efficacy of the approach is demonstrated by measuring temperature changes within a droplet-based PCR device.