Studies in surface science have yielded many perspectives and techniques to solve the two biggest issues in the synthesis of two dimensional materials: degradation during transfer and restriction of applying functional substrates. Atomic manipulation of the surface environment is considered as an essential factor to solve these issues. For example, for the synthesis of graphene, an extremely clean surface can modify the substrate catalytic activity, assist uniform nucleation and avoid structural defects, which can improve the quality of graphene. In addition, many surface treatment techniques have shown great potential for achieving smooth and clean surfaces via physical and chemical etching methods while providing sufficient energy for precursors to decompose, which could potentially avoid the transfer process and enable the use of dielectric substrates at low temperatures. In all, an extremely clean surface is key to the success of direct synthesis of high quality 2D materials on functional substrates in different shapes. (C) 2018 Elsevier Ltd. All rights reserved.