If you want to maintain the same folder structure in your new reference manager, you should export your citations from RefWorks one folder at a time.

It's recommended that you save each export file created below with the name of the folder, so each is easily identifiable when importing to your new reference manager.

1. Login to your Legacy RefWorks account.
2. Click the Organize & Share Folders tab and select a folder for export from the list.
3. Select References > Export (upper left of screen)
4. Choose the following options:

References to Include: 

• All in List (If you have too many references, RefWorks will recommend you export them no more than 500 at a time)
• Select an Export Format: Bibliographic Software 

• Click Export References

5. Your output will open in a separate browser window/tab and will resemble a text file.
6. Use your browser's menu (icon in upper right) to save it as a text (.txt) file
7. Make note of where you save the file, because you'll need it to import your citations into Zotero.