We have WSUS so we have to do this… I know there is a way to publish DotNet 3.5 via WSUS but this seems quicker for the once off times 3.5 is needed.
First get your Server 2012 R2 ISO and copy this folder
D:\sources\sxs (repace D:\ with whatever your optical drive is) to your desktop
Then open powershell or CMD as admin and run:
dism.exe /online /enable-feature /all /featurename:NetFX3 /source:"c:\users\admin\desktop\sxs"
Thats it! Reboot and you should be all set.