Cleaning a scan basically means making the scans look good.
There are many steps in the process of cleaning a scan:
1. Colour-settings: Make sure the scan is in greyscale mode or, for colour images, RGB mode. [+] [-]
2. Rotating: Rotate the scan to have it aligned correctly. [+] [-]
3. Merging: Connecting two pages that are part of a double page spread. [+] [-]
4. Cropping: Crop out unneccessary parts of the scan. [+] [-]
5. Leveling and dusting: Level the image so the blacks are black and the whites are white without damaging the greys then clean any specks that were left. [+] [-]
6. Redrawing: Complete any necessary redrawing, e.g. restoring the background behind offtexts. [+] [-]
7. Resizing: Resize your image to have a web-compatible size (depending on your group this may not be wanted) [+] [-]
Now we are going to resize the whole thing; this process is pretty quick. Press Controll-Alt-I, set the dpi-number to 72 (this is best for typesetting) if that has not been done yet, and set the height or width to a set number. Most groups always use the same heights settings, some others go by the width. The important point is that all pages of the same chapter, or even better the whole manga, should be resized to a set size.
Depending on your group you may also be required to have the whole chapter/manga have the same height & width settings, for this set the height and afterwards adjust the width using Controll-Alt-C.
8. Cleaning bubbles: Clear the text from the bubbles. [+] [-] [Action]
9. Saving: Save the image. [+] [-]
Other useful stuff pt.1: Adjustment layers. [+] [-]
Other useful stuff pt.2: Training Raws. [Low Quality]