In Zotero, folders are called collections. You will need to create new collections in Zotero that correspond to your folders in RefWorks, however to do this you must move references or folder at a time. However, if you do not care about maintaining this structure, you can migrate your entire RefWorks library all at once.
These instructions are borrowed from the Massachusetts General Hospital Institute of Health Professionals Guide.
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.
If you don't need to maintain the same folder structure in your new reference manager, exporting your citations all at once is a much quicker option.
1. Open Zotero. From the File menu in the upper left hand corner, select Import.
2. A window asking "Where do you want to import from?" will pop up. Select A file and click Next.
3. Select a file you exported from RefWorks and click Open.
4. A dialogue box with the option "Place imported collections and items into a new collection" will appear. You have two choices:
Once you have made your selection, click Next.
5. Your references are now imported into Zotero.