Highly ordered silver nanopore and nanocap arrays, which were used as surface-enhanced Raman scattering active (SERS-active) substrates, were fabricated by electron-beam evaporating silver on the surface of porous layer and barrier layer of porous anodic alumina (PAA) membranes, respectively. The SERS characteristics of the SERS-active substrates were tested with bladder cancer cells as molecular probe. The results indicated that both the SERS-active substrates displayed a strong SERS enhancement effect. The silver nanocap ordered arrays SERS-active substrate displayed not only higher SERS and fluorescence quenching effect, but also no interferential spectrum related with oxalate impurity remaining in PAA membranes, and therefore can result in the high quality Raman spectroscopy of bladder cancer cells.