A template manufacturing method includes preparing a structure including a first substrate and a stacked body that is provided on the first substrate, the stacked body including a first lower layer including a first material, a first upper layer provided on the first lower layer including a second material different from the first material, and a first cover layer provided on a first cover region of the first upper layer and including a third material different from the second material. The method further includes forming a first resist layer on a portion of the first cover layer and on a first portion of the first upper layer, and exposing a second portion of the upper layer. The method yet further includes removing the second portion of the first upper layer using the first cover layer and the first resist layer as a mask.