Cell cultures and tissues often contain cellular subpopulations that potentially interfere with or contaminate other cells of interest. However, it is difficult to eliminate unwanted cells without damaging the very cell population one is seeking to protect, especially established tissue. Here, we report a method of eliminating a specific subpopulation of cells from a mixed 2D or 3D cell culture in vitro and a mixed-population in vivo tumor model by using antibody-photosensitizer conjugates (APC) with a near infrared (NIR) phthalocyanine-derivative (IRdye700DX, IR700) combined with NIR light exposure with minimal damage to non-targeted cells. Thus, APC combined with NIR light exposure holds promise as a method of removing specific cells from mixed cell cultures and tumors.