According to one embodiment, a pattern forming apparatus includes a stage provided under a lower surface of a substrate, a probe provided above an upper surface of the substrate, a drive unit which drives at least one of the stage and the probe, a monitor/lithography unit connected to the probe, and a control unit which controls the drive unit and the monitor/lithography unit. The control unit is configured to change a relative position between the probe and the substrate, and form a first pattern in an area direct above a second pattern after detecting the first pattern in the substrate by the probe.