In the past several decades, significant progress has been made to improve the performance of semiconducting light emitting diodes (LEDs), which has resulted in a wide number of applications for LEDs in the information and energy fields. However, light extraction efficiency is limited due to remarkable total internal reflection on the device's surface due to the large refractive index of GaN and indium tin oxides (ITO). In this work, ITO bump and pit patterns were fabricated on the LED surface using an ion beam etching method via metal or resist masks, respectively. By changing the incident angle of the ion beam and the material of the masks, the effects of faceting and redeposition can be properly controlled, resulting in well-controlled manipulation of the shape of the fabricated bump/pit structures. By altering the etching time, the over-etched structures have a much smoother surface compared with the under-etched/in-etched structures. These bump/pit structures could have potential applications in LED light emitting enhancement and optical devices.