Cellulose membranes were obtained by solutions of cellulose being cast into a mixture of N-methyl-morpholine-N-oxide (NMMO) and water under different processing conditions. Atomic force microscopy (AIM) was used to investigate the surface structures of the membranes. The AIM method provided information on both the size and shape of the pores on the surface, as well as the roughness of the skin, through a computerized analysis of AIM micrographs. The results obtained showed that the surface morphologies were intrinsically associated with the permeation properties. For the cellulose membranes, increasing the NMMO concentration and the temperature of the coagulation bath led to higher fluxes and lower bovine serum albumin rejection. These were always correlated with higher values of the roughness parameters and larger pore sizes of the membrane surfaces. When the cellulose concentration of the casting solution was 11 wt %, the membrane showed a nodular structure with interconnected cavity channels between the agglomerated nodules.