While lipid extraction from wet microalgae has attracted attention as an economical method for microalgal biofuel production, few studies have focused the actual separation of extract phase from the emulsified extraction mixture. Here, a novel approach which utilizes hydrophobic/oleophilic filter was developed for the efficient solvent recovery. The filter was surface-modified by coating a functional polymer via initiated vapor deposition for the selective solvent permeability. While acid-treated Chlorella sorokiniana HS1 and n-hexane was stirred for lipid extraction, tubular filter module was immersed into the mixture for separation. The mixture was kept stirred during the separation to inhibit the buildup of cell debris on the filter by inducing crossflow on the filter. Extract phase was separated directly from the raffinate phase with high separation efficiency (> 98.3%) while maintaining permeation flux. The place-, space- and energy-efficient strategy reported here could be a useful tool for the solvent extraction process.