Precise fluorescence-guided surgery (FGS) for pancreatic cancer has the potential to greatly improve outcome. In order to achieve this goal, we have used genetic reporters to color code cancer cells and stroma cells in a patient-derived orthotopic xenograft (PDOX) model. The telomerase-dependent green fluorescent protein (GFP) containing adenovirus OBP401 was used to label the cancer cells of the pancreatic cancer PDOX. The PDOX was previously grown in a red fluorescent protein (RFP) transgenic mouse that stably labeled the PDOX tumor microenvironment bright red fluorescent. The color-coded PDOX model enabled FGS to completely resect the pancreatic tumors including the tumor microenvironment. Dual-colored FGS significantly prevented local recurrence, which bright-light surgery (BLS) or single color surgery could not. FGS, with color-coded cancer and the tumor microenvironment has important potential for improving the outcome of recalcitrant cancer.