The flux behavior of 0.2 μm nylon, polysulfone (PS), polyvinylidene fluoride (PVDF) and polyethersulfone (PES) membranes was examined during dead-end microfiltration of commercial apple juice. On nylon membranes, a 0.1 μm thick surface fouling layer rapidly formed that acted as a secondary membrane. The colloidal particles retained by this surface layer aggregated to form a thick loose gel structure, producing an anisotropic fouling structure. In contrast, the 4 μm thick surface fouling layer of PES was slower to form and had a more open structure with a lower flux resistance per unit thickness. The morphology of the PES surface layer also did not differ dramatically from the loose gel structure that subsequently formed on top of this secondary membrane. The PS surface fouling layer was similar in structure to nylon whereas the PVDF layer more closely resembled that found with PES. The density of the surface fouling layer did not directly correlate to membrane surface hydrophobicity or pure water flux. Atomic force microscopy (AFM) indicated that surface roughness strongly influenced surface fouling layer morphology. The membrane surface appears to act as a template for the fouling process; therefore, smooth membranes (nylon and PS) produce a dense surface fouling layer whereas this same layer on rough membranes (PES and PVDF) is much more open. Consequently, the fluxes of PES and PVDF membranes are less affected by fouling formation.