A method for heating a substrate in a vacuum environment and a system therefor is provided. The system includes a chamber capable of holding the substrate located in the vacuum environment and a light source capable of projecting a light beam only on a portion of the substrate. The method includes the following steps. First, the substrate is placed in the vacuumed chamber. Thereafter, the light beam emitted from the light source is projected on the portion of the substrate, such that the portion is significantly heated before whole the substrate is heated. When the light beam is a charged particle beam projected by a charged particle beam assembly and projected on defects located on the substrate, the defects are capable of being identified by an examination result provided by an examination assembly after termination of light beam projection.