In accordance with an embodiment, a marking apparatus includes a charged particle beam device and a marking unit. The charged particle beam device generates a charged particle beam, irradiates a sample including a laminated body with the charged particle beam, detects secondary charged particles generated from the sample, and acquires a sample image. The marking unit bores a hole reaching at least a second layer from a surface layer in the laminated body in a viewing field of the charged particle beam device.