Focal adhesions (FAs) are mechano-sensitive elements that mediate cellular response to applied forces and scaffold material properties. The microstructure of FAs has been investigated with several approaches that include super-resolution fluorescence microscopy, cryo-electron tomography, and atomic force microscopy (AFM), but the contribution of α-actinin to forming the architecture remains unclear. Here we combine AFM with fluorescence microscopy to investigate the 3D geometry of FAs together with observation of fluorescent α-actinin expressed within cells. A7r5 cells, an embryonic aortic smooth muscle cell line, are cultured on a glass-bottom culture dish and de-roofed with a hypotonic treatment to allow their FAs to be accessed by an AFM probe. Our observations show that α-actinin-1, one of the isoforms expressed at FAs within the cells, contributes to layering of actin filaments toward the direction of the height rather than the cross-linking of individual actin filaments within planes.