OMR sheets can be filled using a pen or a pencil, as instructed. Most examination committees stick to use of pens exclusively, while some do allow the use of pencils. You cannot simply use any type of pen for filling the sheets. Stick to ball point pens only, as fountain pens and gel based pens can cause unnecessary smudging of wet ink and may cause stray pen marks on the OMR sheet. Moreover, also the color of the pen is of much significance here. All OMR software are based on the concept of contrasting colors. The OMR software detects and reads dark marks on the OMR sheets to determine the accuracy of the candidate's answer responses.
For filling OMR sheets, ideally black and blue colors are preferred. Red and green are avoided as these are lighter colors.
When you introduce the scanned images of OMR sheets in the OMR software, all colors except for black and blue are automatically dropped. Black and blue marks are read as black, while red and green shades turn grey, which is not read by the software.
Also, the colors green and red are not preferred for filling OMR sheets, as the red colored pens are usually used by examiners to check the answer sheets and allocate marks; Green is generally used by the exam supervisors or institute HODs.
These are the prime reasons why most exam committees instruct the students to use black or blue pens for filling OMR sheets. If it is specifically instructed that you use either blue or black pen, use only that color of pen.