Solved Virus: apps won't launch (.exe files)

Riotubes

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I've run microsoft security essentials, malwarebyt's anti-malware and ccleaner in regular and safe mode and can't seem to pick up the virus/trojan that has disabled all my apps (MS office, firefox browser, MSE, etc.). I can get MSE to run (as administrator). When I launch any app, like microsoft word, I get a window that says "app not found".

I also tried reverting to an earlier restore point, but unfortunately they don't go far enough back prior to the issue.

How can I fix this?
 

My Computer My Computer

OS
Win7 Pro 64-bit
CPU
i7 870
Motherboard
Gigabyte GA-55A-UD3
Memory
16GB
Graphics Card(s)
FireGL 4800
Hard Drives
90 GB OCZ Vertex 2 SSD
1TB Samsung Spinpoint F3R
PSU
Antec Tru Power 650W
Case
Lian Li

My Computer My Computer

Computer type
PC/Desktop
Computer Manufacturer/Model Number
Golden Mk. I.4
OS
Windows 10 Pro x64 ; Xubuntu x64
CPU
Intel i7 860 @ 2.80 GHz O/C'ed to 4.0GHz
Motherboard
Gigabyte P55A-UD3R Rev.1. Award BIOS F13
Memory
16GB Corsair Vengance DDR3 @ 661 MHz Dual Channel (9-9-9-24)
Graphics Card(s)
EVGA NVidia GTX 560 1024MB
Sound Card
Realtek Integrated
Monitor(s) Displays
Dual Samsung SyncMaster 2494HS
Screen Resolution
1920*1080 and 1920*1080
Hard Drives
1*Samsung 840 EVO 120GB SSD;
1*OCZ Vertex 2 60GB SSD;
2*Samsung F3 SpinPoint 1TB in RAID0;
1*Samsung F1 SpinPoint 1TB;
2*Western Digital 1TB External USB 3.0
1*Western Digital 500GB External USB 3.0
1*Seagate 500GB External USB 2.0
PSU
Thermaltake ToughPower QFan 750W
Case
Thermaltake Element S VK60001W2Z
Cooling
Corsair H60 Water Cooling, 2*230mm and 2*80mm case fans
Keyboard
Logitech G110
Mouse
Logitech MX518
Thank you. Your linked worked perfectly. Yes, I did have a trojan quarantined by MSE but I inadvertently deleted the history. Also, the Update does not work on malwarebytes which, in the past, has been a good indicator of a virus.
 

My Computer My Computer

OS
Win7 Pro 64-bit
CPU
i7 870
Motherboard
Gigabyte GA-55A-UD3
Memory
16GB
Graphics Card(s)
FireGL 4800
Hard Drives
90 GB OCZ Vertex 2 SSD
1TB Samsung Spinpoint F3R
PSU
Antec Tru Power 650W
Case
Lian Li

My Computer My Computer

Computer type
PC/Desktop
Computer Manufacturer/Model Number
Golden Mk. I.4
OS
Windows 10 Pro x64 ; Xubuntu x64
CPU
Intel i7 860 @ 2.80 GHz O/C'ed to 4.0GHz
Motherboard
Gigabyte P55A-UD3R Rev.1. Award BIOS F13
Memory
16GB Corsair Vengance DDR3 @ 661 MHz Dual Channel (9-9-9-24)
Graphics Card(s)
EVGA NVidia GTX 560 1024MB
Sound Card
Realtek Integrated
Monitor(s) Displays
Dual Samsung SyncMaster 2494HS
Screen Resolution
1920*1080 and 1920*1080
Hard Drives
1*Samsung 840 EVO 120GB SSD;
1*OCZ Vertex 2 60GB SSD;
2*Samsung F3 SpinPoint 1TB in RAID0;
1*Samsung F1 SpinPoint 1TB;
2*Western Digital 1TB External USB 3.0
1*Western Digital 500GB External USB 3.0
1*Seagate 500GB External USB 2.0
PSU
Thermaltake ToughPower QFan 750W
Case
Thermaltake Element S VK60001W2Z
Cooling
Corsair H60 Water Cooling, 2*230mm and 2*80mm case fans
Keyboard
Logitech G110
Mouse
Logitech MX518
I ran malwarebyts again and it picked up

trojan.fakealerts affecting registry value

HKEY_CURRENT_USER\SOFTWARE\Microsoft\Windows\CurrentVersion\Run\3561584484 (Trojan.FakeAlert) -> Value: 3561584484 -> Quarantined and deleted successfully.
 

My Computer My Computer

OS
Win7 Pro 64-bit
CPU
i7 870
Motherboard
Gigabyte GA-55A-UD3
Memory
16GB
Graphics Card(s)
FireGL 4800
Hard Drives
90 GB OCZ Vertex 2 SSD
1TB Samsung Spinpoint F3R
PSU
Antec Tru Power 650W
Case
Lian Li
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