In manufacturing a thin film transistor array substrate, a passivation film is formed over the transistors. A first photoresist pattern is formed over the passivation film, with a first portion partially overlying at least one source/drain electrode of each transistor and overlying each pixel electrode region, and with a second portion thicker than the first portion. The passivation film is patterned using the first photoresist pattern as a mask. The first photoresist pattern's first portion is removed to form a second photoresist pattern which protrudes upward around the pixel electrode regions. A transparent conductive film is formed with recesses in the pixel electrode regions. A masking pattern is formed over the transparent film in each pixel electrode region, the masking pattern's top surface being below a top of the transparent film. The transparent film is patterned using the masking pattern as a mask to form the pixel electrodes.