A method of manufacturing a semiconductor device, includes forming a trench in a semiconductor substrate having a first face and a second face by processing the first face of the semiconductor substrate, the trench including a first portion and a second portion located between the first portion and a plane including a first face, filling an insulator in the second portion such that a space remains in the first portion and the trench is closed, and forming a plurality of elements between the first face and the second face, wherein the space and the insulator form element isolation.