Wolfram Language is a programing language, not a tool like Gimp or Photoshop. You need to write code, actual functions that process things. That is typing and copy-pasting. Interactivity in 3D is present, but not for pixel mask yet I think, this would be hard, I am not sure how that would work. Perhaps Image3DSlices should help you somehow with 3D version.

Please, consider filling out your profile: @Subhrajyoti Maji. I think what you are asking is building a mask interactively. You can choose whether use the mask as an image or list of pixels. Tutorial below shows how to use ti as image and then use it in a image processing operation further. Explore interactive interface shown in the video to see other options. It is called Interactive Image Assistant - see more details at the link.