Provided are semiconductor integrated circuit (IC) devices having an upper pattern aligned with a lower pattern molded by a semiconductor substrate and methods of forming the same. In the semiconductor IC devices, the lower pattern contacts the upper pattern using an active region and/or an isolation layer. The methods include preparing a semiconductor substrate having an active region. A lower pattern is formed on the active region. The lower pattern is surrounded by the active region and protrudes from a top surface of the active region. An upper pattern is disposed on the lower pattern. The upper pattern contacts the lower pattern.