PREPERATION
First of all, you have to make sure you scanner's surface is clean, get a soft cloth and gently wipe it, getting rid of any dust that may have settle on the surface. You may want to use some Spray and Wipe or Windex if there are marks on your scanner glass, but make sure you wipe the glass dry before you place down the cover.
Make sure the cover is straightened in the corners of your scanner - If the cover is out of line, use Photoshop's straightening technique which will allow you to rotate it down to 0.01 degrees if you need to, which is alot more precise than most image editing software...
FLATTENING OUT THE COVER
Then make sure that the cover is perfectly flat, I use a my Lord of the Rings heavy hard-cover book to clamp the cover down, phone books also work well, but I would recommend a hard cover book. This extra weight will not damage your scanner, it will just flatten the cover more than it would have been originally, giving you a much better scan.
Now your ready to go! - Scan the cover following the regulations below...
Covers - Originally scan the cover at 600dpi, this should give you an approx resolution of 6480x4350. Then open in Photoshop (or which ever program you like to use) and apply the apropriate filters (SEE HALFTONE DOTS FOR MORE) then resize it down to 3240x2175 at 300dpi AFTER APPLYING FILTERS.
Labels - Originally scan the label at 600dpi, this should give you an approx resolution of 2800x2800. Then resize that down to 1400x1400.
I will assume the majority of people are using Photoshop, since that is the feedback i got from my poll on the topic.
STRAIGHTENING UP THE COVER
Open up your 600 dpi scan in Photoshop, go to the toolbar on the left-hand side of the screen. Find the Eyedropper tool, right-click it and select Measure Tool. When the measure tool is selected, view the scan at Actual Pixels. Then click and hold the measure tool from one corner of the cover down to another corner. Then go to Image --> Rotate Canvas --> Arbitrary. Click OK and the cover will now have been rotated so it is perfectly straight.
Then go to Image --> Rotate Canvas --> 90 CW or 90 CCW depending on which way you scanned your cover. Select the one which applies to you and your scan will now be perfectly straight.
CROPPING
Then go to the select tool on the toolbox. Select a rectangular shape around the border of the cover, try to chop off as little of the original cover as possible when doing this. Then go to Image --> Crop.
HALFTONE DOTS
Now we will try and get rid of the Halftone Dots while still keeping as much quality as possible. Go to Filters --> Blur --> Gaussian Blur. Set the radius from 0.8 - 1.0 but no higher or lower. Try not to blur the image too much...just enought to be able to rescue it later on.
Then go to Filters --> Noise --> Despeckle. Make sure your scan is still 600 dpi (6480x4350) then apply the Despeckle filter 2 times, because the image is larger, we need to apply this filter more, but DONT apply it more than 3 times, otherwise you will lose too much information and the cover will look too edited.
Then resize your cover down to 3240x2175, with 300 dpi
Then go to Filters --> Sharpen --> Unsharpen Mask. Set Ammount to 60%, Threshold to 1, and the Radius to anywhere from 1.2-1.6 but no higher. I would recommend 1.4 because I feel this is the ideal setting.
SAVE YOUR WORK
File --> Save the image at number 12 quality setting in Photoshop. And Your Done!
