Fluorescence Resonance Energy Transfer (FRET) is a standard technique used in many medical and biological applications. It involves the detection of transient fluorescent signals coming from the different fluorescent proteins that work in the visible range of the spectrum. Common fluorescent emissions come from the cyan/yellow fluorophores that emit respectively, at 470 nm and 588 nm. In this paper we use optical filters based on multilayered a-SiC:H heterostructures to detect optical signals at these wavelengths. The advantage of this type of sensor is that it does not rely on mechanical parts; it is compact and cost effective. The transducer consists of two heterostructures based on a-SiC:H/a-Si:H optimized for the detection of the fluorescence emissions at wavelengths 470 nm (cyan) and 588 nm (yellow). Both front and back structures were designed to optimize the detection at these wavelengths. Results show that the device photocurrent signal measured under reverse bias and using appropriate steady state optical bias, allows the separate detection of the cyan and yellow fluorescence signals.