From MozillaZine Knowledge Base
This article gives step by step instructions for how to import folders from another profile for a new user who has never installed an extension. It assumes you're using Windows but you should still be able to follow the instructions using a file manager on another operating system. The ImportExportTools extension can also be used to export folders, though this article doesn't describe how to do that.
Install the ImportExportTools extension
Find your old profile
Your folders are stored as mbox files in a profile. These are text files with the folders name and no file extension. For example your inbox folder is the "inbox." file and the Sent folder is the "Sent." file. You can safely read one using a text editor to verify it contains mail messages though its not user friendly because it contains the raw message source, including all of the headers and big blocks of characters all run together whenever you have a binary attachment.
If you're running Windows 2000 or later you may need to enable "Show hidden files and folders" and disable "Hide extensions for known file types" (its under the Hidden files and folders heading) and "Hide protected operating system files (Recommended)" in Tools -> Folder Options -> View to see it. You may get a warning message that your computer won't work if you do this. Changing those settings causes no harm, its really warning you not to change or delete any of the files or directories used to store the operating system. See this thread if you're running a older version of Windows.
Find the folders
If the folder was in Local Folders or you used a global inbox it will be somewhere in the Mail\Local Folders directory within the profile. Otherwise look for a subdirectory named after the accounts mail server. For example, if you're using a Gmail POP account your inbox would normally be the "inbox." mbox file at Mail\pop.gmail.com. If you have multiple accounts with the same email provider the subdirectory might have a numeric suffix, for example Mail\pop.gmail-2.com.
Ignore the .msf files, they don't have any messages. You want the files with the folders name and no file extension.
Thunderbird uses *.sbd subdirectories to create a folder hierarchy. So a Local Folders\1\2\xyz folder would be stored as a "xyz." mbox file at Mail\Local Folders\1.sbd\2.sbd\3.sbd . That directory would also have a empty xyz.sbd subdirectory created in preparation for you someday creating a child folder of xyz. Ignore it.
Import the folders
Your folders are stored as mbox files in a profile. These are text files with the folders name and no file extension. For example your inbox folder is the "inbox." file. DO NOT try to import "inbox.msf" or "inbox.sbd" - the messages are in "inbox.". That naming convention causes a lot of confusion, it would have been a lot easier if the mbox files had a .mbx or .mbox file extension like some other email clients use.
Tools -> ImportExportTools -> Import Messages and "Import all messages from a directory" import .eml files. Thunderbird doesn't store messages using .eml files. That is mainly used for import messages from other email clients that don't support mbox files.