The flat sheet polyethersulfone (PES) and poly(vinylidene fluoride) (PVDF) membranes were prepared by immersion precipitation technique. The influence of hot air and water treatment on morphology and performance of membranes were investigated. The membranes were characterized by AFM, SEM, cross-flow filtration of milk and fouling analysis. The PES membrane turns to a denser structure with thick skin layer by air treatment at various temperatures during different times. This diminishes the pure water flux (PWF). However the milk permeation flux (MPF) was considerably improved at 100 °C air treatment for 20 min with no change in protein rejection. The smooth surface and slight decrease in surface pore size for air treated PES membrane at 100 °C compared to untreated membrane may cause this behavior for the membrane. The water treatment of PES membranes at 55 and 75 °C declines the PWF and MPF and increases the protein rejection. This is due to slight decrease in membrane surface pore size. The treatment of PES membrane with water at higher temperature results in a porous structure with superior performance. The fouling analysis of 20 min treated membrane indicates that the surface properties of 100 °C air treated and 95 °C water treated PES membranes are improved compared to untreated membrane. The SEM observation depicts that the morphology of air and water treated PVDF membranes was denser and smoother with increasing the heat treatment temperature. The 20 min air treated PVDF membranes at 100 °C and water treated at 95 °C exhibited the highest performance and antifouling properties.