The unique ability of the ultrafast lasers to perform sub-spot size machining has been proved to be advantageous over conventional lasers for sub-micron-machining. To achieve this, a Gaussian laser beam free of spatial defects is essential. In this research work, submicron holes with clear edge and symmetric shape on thin metal films using a Ti:Sapphire regenerative amplified femtosecond pulsed laser are produced. While analysing, it is observed that there are two shallow pits accompanying the produced hole, symmetrically located at the two sides of the hole, especially when the holes are in the sub-micron range. A careful study on the effects of these shallow pits and the methods to eliminate the same are presented in this letter. It has been concluded that the shallow pits are Rowland ghosts raised by deficiencies of grating space present in the two pairs of gratings used for pulse stretching and compressing. Methods of eliminating these ghosts to achieve features with better edge acuity and quality are also presented.