Cell-repellent interfaces have various applications, including microfluidic devices, biosensors, and antibiofouling surfaces. Efficient cell repellency, long-term stability, and ability to fabricate micropatterns with cell repellency are main optimal requirements for cell-repellent interfaces. In this study, a flexible and practical method is proposed to construct a cell-repellent interface and engineer controlled cell organization. Using femtosecond-laser direct writing to pattern surfaces with microcraters, it is shown that micropatterned surfaces with physical and chemical changes have outstanding characteristics of super-hydrophobicity. Furthermore, the cell adhesion is inhibited by these features and arbitrary cell patterns are achieved by selective cell adhesion induced by the distribution of the microcrater structures. These findings suggest a high potential for directing cell organization with desired shapes to analyze the fundamental mechanism of cell adhesion.