The shifted-contour auxiliary-field Monte Carlo (SCAFMC) approach has been recently developed by Rom, Charutz and Neuhauser as an extension of the auxiliary-field Monte Carlo (AFMC) method. AFMC replaces the difficult fully interacting electrons problem by an ensemble of simpler problems where the electrons interact with a fluctuating electric field but not with each other. SCAFMC is based on shifting the auxiliary-field contour of integration to pass through the (imaginary) stationary point, leading to numerical stability at long propagation times. The new approach converges to the full CI energy in electronic structure calculations (both ground and low-lying excited states). Here we expand the application of SCAFMC from atomic to molecular problems. First, we calculate ground-state energies of a highly correlated transition-metal system (Cr-2) with a moderate (12 orbitals) active space size, and demonstrate that SCAFMC is able to extract the energies accurately. In addition, we use SCAFMC to calculate a C-C bond-stretch energy in ethane with complete active spaces of up to 28 orbitals.