You can filter mailboxes with the F3 license assigned by leveraging the corresponding mailbox plan value. Mailbox plans in Exchange Online determine the quota and settings on newly provisioned mailboxes, depending on the license assigned. You can view the available plans in your tenant via the Get-MailboxPlan
cmdlet. In the case of F3 licenses, we are interested in the "deskless" plan.
To filter only the mailboxes with F3 plan, you can use this:
Get-Mailbox -MailboxPlan ExchangeOnlineDeskless -ResultSize Unlimited