Data corresponds to the demonstration of a novel self-aligned method to fabricate transistors and van der Waals heterojunctions based on 2D materials. Monolayer MoS2 is grown by chemical vapor deposition, and few-layer black phosphorus is mechanically exfoliated and transferred on top of MoS2. For self-aligned transistors, a dielectric extension is obtained by using natural undercut in photoresist and e-beam resist profiles. The channel length of ~150 nm is obtained, and resulting devices showed better current saturation than the literature reports on conventional short-channel transistors. The observed behavior is due to a source-gating effect, as verified by commercial device simulator Sentaurus TCAD. Similarly, BP-MoS2 heterojunction diode showed significantly better electrostatic control than lateral or vertical heterojunction between these two semiconductors. This behavior, as verified from device simulator, also originates from the novel self-aligned structure. The approach is generalized to mixed dimensional heterojunction between pentacene-MoS2.