Hello, am very concerned here by several things you said,
First:Microsoft security essentials detected threats and then you said first thing I did was run avira scan
Are you saying that you have BOTH of these programs running on your computer? If so that is a BIG No-No. Both are anti-virus programs and the absolute rule is ONE anti-virus program should be running on a computer, never two. Uninstall one of these Immediately.
Second thing you say I find concerning, so I ran malwarebytes and that said it found 2 and when I hit remove it said one couldn't and needed a restart, but you did NOT restart but instead tried to open a browser. Instructions for malwarebytes' are very clear, REBOOT after running MBA-M!The reason for this request by malwarebytes is that the program cannot fully remove many infections except during the reboot process when the infected file is not yet in use. It is obivious by booting to safe mode instead of the normal reboot that the malwarebytes' removal was not complete because you said the process showed in the HJT log. Was it running or in start ups or where? I need to see that HJT log.
I need especially to see the log from that very first malwarebytes' scan, which can be found by opening the program, going to the Logs tab and it is likely it will be the bottom log on the list. Post that log immediately.