Disclosed is the preparation of composite membranes formed by a tailored selective chemical modification of an ultra-thin nanoporous surface layer of a semi-crystalline mesoporous poly (aryl ether ketone) membrane with graded density pore structure. The composite separation layer is synthesized in situ on the poly (aryl ether ketone) substrate surface and is covalently linked to the surface of the semi-crystalline mesoporous poly (aryl ether ketone) membrane. Hollow fiber configuration is the preferred embodiment of forming the functionalized the poly (aryl ether ketone) membranes. Composite poly (aryl ether ketone) membranes of the present invention are particularly useful for a broad range of fluid separation applications, including organic solvent ultrafiltration and nanofiltration to separate and recover active pharmaceutical ingredients.