Although existing methods (chemical vapor deposition, mechanical exfoliation, etc.) are available to produce graphene, the lack of thickness control limits further graphene applications. In this study, we demonstrate an approach to precisely thin graphene films to a specific thickness using femtosecond (fs) laser raster scanning. By using appropriate laser fluence and scanning times, graphene thinning with an atomic layer precision, namely layer-by-layer graphene removal, has been realized. The fs laser used was configured in a four-wave mixing (FWM) system which can be used to distinguish graphene layer thickness and count the number of layers using the linear relationship between the FWM signal intensity and the graphene thickness. Furthermore, FWM imaging has been successfully applied to achieve in situ, real-time monitoring of the fs laser graphene thinning process. This method can not only realize the large-scale thinning of graphene with atomic layer precision, but also provide in situ, rapid imaging capability of graphene for an accurate assessment of the number of layers.