Many download managers and backup programs allow you to scan files with a virus scanner, using the command line. In this way, you can use Luke Filewalker, the graphical user interface of AntiVir software, configuring it with the following parameters:
(the syntax is not case-sensitive, but the paths have to be inserted in double-quotes)
/CFG="<path to the scan profile file>"
/PATH="<path to the folder or file to be scanned>"

Examples:
"%PROGRAMFILES%\Avira\AntiVir Desktop\avscan.exe"  /CFG="%PROGRAMFILES%\Avira\AntiVir Desktop\scan.avp"
"%PROGRAMFILES%\Avira\AntiVir Desktop\avscan.exe"  /PATH="%WINDIR%"
"%PROGRAMFILES%\Avira\AntiVir Desktop\avscan.exe"  /PATH="C:\Downloads\"
"%PROGRAMFILES%\Avira\AntiVir Desktop\avscan.exe"  /PATH="C:\Downloads\%1"

AntiVir Scanner uses the configuration set in AntiVir, under Configuration - Scanner. So, if you activated the option Scan master boot sectors, they will be scanned every time avscan.exe starts.

In case you do not want to use this option, because the scanning takes longer, there is a work-around, for scanning only the selected files.

1. Download this profile file (right-click the link and select Save link as): filescan.avp
2. Save the file on your hard disk, then right-click it and select Properties. Activate the option Read only and press OK.
3. Now you have to apply this profile to the /CFG parameter. For example, to use AntiVir with WinRAR, you have to use the following parameters:
   Scanner name: "%PROGRAMFILES%\Avira\AntiVir ...\avscan.exe"
   Scanner parameter: /CFG="C:\filescan.avp" /PATH="%f"

You can also use Avira AntiVir Command Line Scanner (AVCLS) which has detailed configuration possibilities. It can be downloaded from Avira website, under Support - Downloads. Please read the installation guide and the description of the parameters in the downloaded text file.