Alureon.s has infected and screwed my computer up, help?

i got a trojan called alureon.s, and windows security essentials deleted it and asked to restart my computer. when i turned it back on all my shortcuts had disappeared, and i cant access programs from the start menu. fortunately i can still access files through explorer and through toolbars on the task pane. i retrieved some of my desktop shortcuts when i clicked "show hidden files" in the folder options tab. but still half of them are missing and i cant access them in the start pane. it just says empty, when i click on show all programs. how do i fix it?? i dont have a restore point set up on windows yet, so that won't help.