My system was running out of disk space so I checked and found out that Mail is occupying close to 3 GB of disk space. The Mail app is about 40 MB and the restare the files locally downloaded from the Mail. How can I delete these files without affecting the original mails?
What email is the Mail app using? If its not iCloud then you can easily manage how much email is sent to your Macbook directly from the clients website (Gmail, Yahoo, Aol, & etc). If it is iCloud email, then you may want to manage whats coming in. You can also turn mail off and on under iCloud in system preferences.
Open System Information from the Utilities folder in /Applications. Choose the menu item Window → Storage Management, then choose Mail. Follow the instructions to remove downloaded attachments.