Limited access to tumor tissue makes repeated sampling and real-time tracking of cancer progression infeasible. Circulating tumor cells (CTCs) provide the capacity for real-time genetic characterization of a disseminating tumor cell population via a simple blood draw. However, there is no straightforward method to analyze broadscale genetic rearrangements in this heterogeneous cell population at the single cell level. We present a one-step controllable chemical extraction of whole nuclei from prostate cancer cells captured using geometrically enhanced differential immunocapture (GEDI) microdevices. We have successfully used copy number profile analysis to differentiate between two unique cancer cell line populations of metastatic origin (LNCaP and VCaP) and to analyze key mutations important in disease progression.