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) [+] [-]
8. Cleaning bubbles: Clear the text from the bubbles. [+] [-] [Action]
9. Saving: Save the image. [+] [-]
This should be clear: press Controll-S, save the image in .psd format and do not flatten the layers (This keep all the different layers intact for other people to see/edit). Now you can feel refreshed, you just cleaned a page.
Other useful stuff pt.1: Adjustment layers. [+] [-]
Other useful stuff pt.2: Training Raws. [Low Quality]