Malignant cancer cells constantly interact with their surrounding environment and migrate by remodeling the local extracellular matrix (ECM). A quantitative understanding of the remodeled ECM can provide new insights into the process of metastasis. Cells suspended in 3D matrices can mimic many of the physicochemical and mechanical properties of tumors in vivo. Our system is designed to approximate the in vivo histopathological milieu of a malignant breast tumor. Nanorobots can be effective tools for studying cellular biophysics and probing the local rheology of biological systems. Here we demonstrate how magnetically actuated helical nanorobots can probe a 3D tissue co-culture consisting of both cancerous and non-cancerous cells. We find that nanorobots adhere preferentially near cancer cells due to the distinct charge conditions of the cancer-sculpted ECM. The spatial extent of the remodeled ECM was measured to be approximately 40 μm for all cells. However, quantitative measurements showed the adhesive force to increase with metastatic ability of the cell lines. We hypothesized and experimentally confirmed that specific sialic acid linkages related to cancer-secreted ECM may be a major contributing factor in determining this adhesive behavior. Cell-line specific anisotropy in sialic acid distribution was also discovered by nanorobots. These findings can lead to promising applications in cancer diagnosis and quantification of cancer aggression.