(This post is kind of long, but only because I've made it rather detailed. It's not nearly as complicated as the length would imply.)
First, make sure the COMPILATION field is visible in the file view (the table of columns on the right). Create a new column by right-clicking the header row and selecting 'Customize columns...'. Then click the 'New' button, enter something like 'Comp' for Title and enter '%compilation%' (without the quotes) for both the Value and Field. Move it up the list so that's it's near the top and so that it will appear on the left in the file view.
To select only the compilation tracks you can either:
Sort by the Comp column by clicking it's column header. Reverse the sort order, if you like, by clicking it again. Select all of the tracks with a value of 1.
or (easier)
Use the Filter capability to only have compilation tracks visible in the file view. Press F3. Enter the following in the Filter box (capitalization of the word 'IS' is required):
compilation IS 1
Make sure it worked by noting the numbers shown in the bottom right box of Mp3tag's status bar. After applying the filter it should show numbers N/M (files in view/total files), with N less than M. Also scroll through the tracks remaining to be sure they all have a 1 showing in the Comp column.
Use the Converter, Tag - Filename feature by using either the 
button, ALT+1, or through the menus Convert > Tag - Filename. Enter something like the following Format string. The part after the last backslash is the file name, so format it the way you like:
M:_VA\%album%$num(%track%,2) %title%
This would give you something like:
M:_VA\Trainspotting\01 Lust for Life.flac
I like to place the artist(s) names into the filename of compilation tracks, since I can't see them in the folder path:
M:_VA\%album%$num(%track%,2) $meta(%artist%) - %title%
An example of what this would produce is:
M:_VA\A Twist of Marley\01 Lisa Fischer, Michael Brecker - Exodus.flac
There may be more in the FAQ:
* As always: Test this several times before applying it to your entire library. I would try it out on a single artist's folder first and I would have a backup of that folder. Once you're sure it works, test on a second and third folder, and only then do the whole library. With directory manipulation, once the files are moved, if it doesn't work exactly like you planned, you might have a hard time finding where the files went and may have to search for them. 