I got a virus, quarantined it now important stuff is missing WTF?

i apparently caught a virus last night and when i saw the first pop up window about how my windows security was @ risk i shut down my laptop and started it up n safe mode. i ran two antivirus software applications and it happened to be two Trojan.agents and a Trojan.fakealert. once the scans were complete i shut down my laptop and started it back up normally just to find out that alot of my stuff that was on my desktop along with pics and what seems like everything on my external hard drive is gone, it's a TB and when i open my computer it says that there is 659 GB free of 931 total GB but when i click on my hard drive it says this folder is empty. i need to get this back im a dj and all of my music was on there can anyone help