Scroll to the Reports and Tools sections under the Recently viewed objects and click on Merge Organizations

1) Enter the keyword to find the organizations to merge. You can use an * as a wildcard search.

2) mark the checkboxes next to the organizations you want to merge, and then click Next.

3) Take note if the organization has customer portal access as you want to leave this as the Master Record in the next Step.   

You can select up to 3 organizations to merge at once. If you need to merge more than three, simply repeat these steps after you have completed the first merge.

In this step you have the option to select the values from the different records that you wish to maintain in the merged record.

Fields highlighted in Blue indicate where a difference in the values is present.

1) If one of the records was marked as Customer Portal in the first step, make sure it is the one marked as "Master Record"

If more than one of the organizations is marked as customer portal, you need to go into the organization records that WON'T be the master - and remove portal access (partner staff licenses) from those contacts BEFORE merging.  Their partner staff license will not automatically transfer to the newly merged organization.   (Remove them first, and then after the merge, grant them partner staff access for the newly merged organization)

For fields that are multi-picklists, such as Population Served and Impact Area, it will not merge the values present in both records. If necessary, you can add the other values from the removed organization to the remaining record after it is merged.

2) Once you have marked all the values you wish to preserve, click Merge.

You will then get a warning message that lets you know that the merging of the records can't be undone, and if you want to proceed. Click OK.

Once the merge has been completed, you will be taken back to the Organization Tab, and the remaining organization will be listed at the top of the Recent Organization. Open the record to confirm that all the changes were made. All the records related to the two previous organizations are now related to this record as well.

Merging records requires permission to DELETE records.  Therefore, only system administrators are able to merge records.

Make it your business practice to have your staff make requests for you to merge duplicates that they find.

OR... you can grant a few selected staff people profile permissions via a permission set, that gives selected users delete permissions for Organizations and contacts.