Yes you can and it's recommended anyway to back up stuff including your complete data files.
The only thing you don't need to backup is built-in or DLC content because that will get loaded automatically if you ever reinstall, and can be forced to reinstall at any time should there be a problem.
You need to use Content Manager to do this.
- Create a custom filter for installed+Category rolling stock, and Built-in false and payware false.
- Highlight all the assets or choose a bunch if have have a lot, right click and choose export to CDP.
You may need to do this in parts if you have a lot of content due to there being a limit to the size of the CDP files. I recommend keeping them under 1GB anyway just to be safe.
- Once you get the actual models, select all, right click and choose view dependencies recursively.
A second window will open up, which will list the dependent parts such as bogies, couplers, sound files etc.
Backup this as well.
As far as external devices go, I recommend an actual hard disk rather than a flash drive. Flash drives don't have the longevity of a hard disk, and are much, much slower writing to.