A three-dimensional (3D) cell culture system has been fabricated using a magnetic force based cell patterning method, demonstrating a facile approach for the analysis of invasive capacity of BALB/3T3/v-src using an magnetic force and magnetite nanoparticles. The 3D cell patterning was performed using an external magnetic force and a pin holder, which enables the assembly of the magnetically labeled cells on the collagen gel-coated surface as array-like cell patterns, resulting in the development of a 3D in vitro culture model. The cells embedded in type I collagen showed a compacted, spheroid like configuration at each spot, and distinct, accelerated cell growth was observed in cancer model cells compared with the control cells. The developed 3D cell culture array was applied to the susceptibility assay of the GM6001 matrix metalloproteinase (MMP) inhibitor, a collagenase inhibitor; a distinct suppression of cell proliferation was observed, while little change was observed in 2D. The developed 3D cell culture array system is useful to assess the effects of pharmacologic and/or microenvironmental influences on tumor cell invasion.