Free up space from your drive after upgrading OS X.
Unless you have done a clean install of OS X, you might want to check your Mail folder to delete any old files that are no longer being used.
Apple Mail stores your data in your User’s Library. Unhide your User’s Library folder and locate Mail folder to get started.
Starting with Lion, the User’s Library is hidden. To unhide: Select the Finder in the Dock. Under Go in the Menu bar > hold down the Option key and you’ll see the Library. More info
In Snow Leopard, Mail stored your data in the Mail folder and Mail Downloads. You’ll notice that all the data is stored as individual files.
Mail Downloads folder is no longer being used. You can delete this folder.
In OS X Lion (10.7) through Yosemite (10.10), Mail data is stored only in the V2 folder. You can delete the files and folders from Snow Leopard and only keep the V2 folder.
Users that have install an add-on like SpamSieve, Tags, Mail Act-On etc will want to keep Bundles and SpamSieve folders.
Your Mail folder in OS X 10.7 through 10.10 would look like this if you had any third party add ons:
In El Capitan, Apple now stores your data in V3 folder. The import process moves all your accounts to V3. If you have successfully upgraded Mail in El Capitan, you can delete the V2 folder.
This shows El Capitan Mail with third party bundles. You can delete the Bundles (Disabled) folder.
See Troubleshooting Apple Mail in OS X 10.11 El Capitan for help upgrading.