Biophysical properties are intimately connected to metastatic functions and aggressiveness in cancers. Especially, cellular stiffness is regarded as a biomarker for the understanding of metastatic potential and drug sensitivity. Here, protease‐mediated changes of cortical stiffness are identified due to the deformation of cytoskeleton alignment at a cortex. For the past few decades, membrane type 1‐matrix metalloproteinase (MT1‐MMP) has been well known as a kernel protease enriched in podosomes during metastasis for extracellular matrix degradation. However, the biophysical significance of MT1‐MMP expressing cancer cells is still unknown. Therefore, the nanomechanics of cancer cells is analyzed by a nanoindentation using a microsphere‐attached cantilever of atomic force microscopy (AFM). In conclusion, the results suggest that MT1‐MMP has contributed as a key regulator in cytoskeletal deformation related with cancer metastasis. Particularly, the AFM‐based nanoindentation system for the monitoring of cortical nanomechanics will be crucial to understand molecular networks in cancers.