The directions should have a screw identification page with pics and descriptions of the screws and what they're for. You may have to also use the quantity to help you sort them out if they seem too similar to tell visually. For instance there's qty of 8 of the m3*4 screws and only a qty of 4 of the m3*5. So if you think you have 5 or 6 m3*5 they're probably m3*4 and you need to find the others for that set.
http://www.tweaktown.com/image.php?image=imagescdn.tweaktown.com/content/7/2/7297_29_cooler-master-mastercase-5-modular-freeform-mid-tower-chassis-review_full.jpg