Tumor heterogeneity is one of the biggest challenges in cancer treatment and diagnosis. A multicolor optical ruler is essential to address the heterogeneous tumor cell complexity. Driven by this need, the current article reports the design of a multicolor long range nanoscopic ruler for screening tumor heterogeneity by accurately identifying epithelial cells and cancer stem cells (CSCs) simultaneously. A nanoscopic surface energy transfer (NSET) ruler has been developed using blue fluorescence polymer dots (PDs) and red fluorescence gold cluster dots (GCDs) as multicolor fluorescence donor and plasmonic gold nanoparticle (GNP) acts as an excellent acceptor. Reported experimental results demonstrated that the multicolor nanoscopic ruler's working window is above 35 nm distances, which is more than three times farther than that of Förster resonance energy transfer (FRET) distance limit. Theoretical modeling using Förster dipole-dipole coupling and dipole to nanoparticle surface energy transfer have been used to discuss the possible mechanism for multicolor nanoscopic ruler's long-range capability. Using RNA aptamers that are specific for the target cancer cells, experimental data demonstrate that the nanoscopic ruler can be used for screening epithelial and CSCs simultaneously from a whole blood sample with a detection capability of 10 cells per mL. Experimental data show that the nanoscopic ruler can distinguish targeted cells from non-targeted cells.