Control of crystal shape is an indispensable step for various applications of crystalline products. However, obtaining the desired crystal shape by conventionally tuning environmental conditions (temperature, additives, etc.) cannot always be reached. Recently, we have developed an innovative approach for spatiotemporal control of crystal growth of proteins and amino acids by locally modifying crystal structure (e.g., formation of screw dislocations) via femtosecond (fs) laser ablation. In this work, to clarify the appropriate laser condition for controlling the shape of single crystals with minimized damage, we first systematically investigated the dependence of pulse duration on laser ablation and crystal growth of l-phenylalanine (l-Phe). By using a laser system with tunable pulse durations from fs to nanoseconds (ns), we found fs laser ablation can offer nanometer-sized, sharp etching of which diameter was smaller than the diffraction limit. By utilizing such nanoprocessing via fs laser ablation for promoting the growth of a targeted crystal face, we successfully demonstrated the preparation of a bulky crystal of l-Phe, which is difficult to be obtained by conventional crystallization methods.