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. [+] [-]
An example for an offtext redraw:
This has already been dealt with in the merging sub-section. By that I will just re-use the text and images. If there is just blacks and whites underneath your offtext, it is quite easy and you can use the brush tool (B).
It is somewhat harder if you have to redraw patterns though. There are two ways of doing that: cloning (S, then click Alt-Key on what you want to see cloned, and draw your mouse over the parts that are supposed to be filled) and using the rectangle tool on the pattern elsewhere (M), then copying it into a new layer(Controll-J) and finally move it to the right place (V); maybe you will be required to erase some of the just copied stuff to fit it into the surroundings using the eraser tool. (E)
In general, pattern redraws are dangerous because you need to fit the newly added stuff completely into the pattern.
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. [+] [-]
Other useful stuff pt.1: Adjustment layers. [+] [-]
Other useful stuff pt.2: Training Raws. [Low Quality]