The directed energy deposition (DED) process has been used for enhancement of the mechanical property, repair, and part manufacturing. Post-process machining is required due to the low quality of the DED printed part. Even if the part is printed under similar conditions, dimensional variations occur frequently due to the accumulation of small printing errors. Due to tool overfeeding and the occurrence of the non-cutting area due to this variation, the quality of the finished part is not guaranteed. Therefore, the post-process machining should be carried out considering the actual printed part shape. Herein, the flexible post-process machining is proposed by utilizing the shape information through the on-machine measurement (OMM) of DED printed parts. The process margin for machining the design shape is calculated through the OMM of the geometric dimension of the printed part. Feedrate (Override) and machining path of each printing parts are flexibly determined depending on the process margin. This technique is applied to the pocket shape part printed with STS 316L material, and the rough and finish machining conditions are established. Rough machining time was reduced by adjusting the feedrate flexibly. The final form of accuracy and surface roughness were achieved under 30 and 0.25 μm, respectively.