A label-free detection strategy for the detection of platelet-derived growth factor (PDGF-BB) oncoprotein detection using signaling aptamer/protein binding complex is reported. The 3D carbon microarrays detection platform was fabricated by pyrolyzing patterned photoresist and surface functionalized using directamination technique. The detection strategy is based on the release of TOTO intercalating dye from the target binding aptamer's stem structure when it captures PDGF. The sensor showed near linear relationship between the relative fluorescence difference and protein concentration with a very good detection limit of 5 pmol. This detection strategy is promising for the potential detection of different cancer biomarkers and proteins.