Temp Folder keeps creating random files that are appearing as Trojan

It is the location for temporary files.  You can see a user's temporary directory by browsing %temp%.
Viruses may create files here as they unpack and be picked up by AV software.  If this does not stop you will need to scan the PC with Antispyware software e.g. Lavasoft Adaware to remove the malware.
You can also run msconfig.exe and check the startup folder.  Some viruses may attempt to installations upon reboot.

Try using Malwarebytes and spybot. They seem to catch additional malware apps that AVs miss.

Run TdssKiller and Hitmanpro.
http://support.kaspersky.com/viruses/solutions?qid=208280684
http://www.surfright.nl/en/hitmanpro

If still having issue run Combofix and post log here
http://www.bleepingcomputer.com/combofix/how-to-use-combofix

First, run a temp file cleaner, TFC (Temp File Cleaner) or any temp cleaner you prefer, CCleaner, ATF Cleaner etc.
http://oldtimer.geekstogo.com/TFC.exe 

Then run the suggested tools like MalwareBytes, TDSSKiller or ComboFix etc and show us the logs.

Please download SuperAntiSpyware Free & Download Hijackthis

http://downloads.superantispyware.com/downloads/SUPERAntiSpyware.exe
www.hijackthis.de

Install the program
Run SuperAntiSpyware and click: Check for updates
Once the update is finished, on the main screen, click: Scan your computer
Check: Perform Complete Scan
Click Next to start the scan.

Superantispyware scans the computer, and when finished, lists all the infections found.
Make sure everything found has a check next to it, and press: Next <-- Important
Then, click Finish

It is possible that the program asks to reboot in order to delete some files.

Obtain the SuperAntiSpyware log as follows:
Click: Preferences
Click the Statistics/Logs tab
Under Scanner Logs, double-click SuperAntiSpyware Scan Log
It opens in your default text editor (such as Notepad)

Please provide the SuperAntiSpyware log in your reply, as well as a new HijackThis log.
Run Hijackthis, install it and run then post your log here please.

You have all given me some great solutions. I appreciate this.

Now can someone please explain to me more about the trojan. How do they keep appearing in temp folder? there being installed from another location?

The temp (%temp%) folder is usually where applications unpack whilst installing.  If you see access denied messages when attempting to clean this folder out it is due to the virus or application locking the file.  Ideally you need to remove the malware so it stops trying to repeatadly reinstall.  Apart from the Endpoint application you should also run other applications e.g. Lavasoft Ad-Aware, Avast Antivirus, Spybot Seach & Destroy, Malwarebytes Antimalware are some that are free.

I believe usually Malware in general likes to use the System restore folder which is hidden in C & D drive and protected from use deletion command.

This is why most of the manual removal instructions would recommend users to disable system restore to delete everything saved within these folders esp malware that keeps generating such files. However it's dangerous to disable system restore since you might need to roll back action in case of failure in any of processes you are applying to get rid of the infection.

Still yet there's another program that does save restore points that runs with Cobmofix.