Filters added during the creating of a bulk migration plan will affect all of the users under your bulk migration plan automatically.
If you choose to migrate files which are 1MB or more, for example, then this filter will apply to all of the users under your migration.
After creating your migration plan, you can change a specific user's filter / security option.
Click on Migration Plans and Multi-User Migration Plans (also known as Bulk).
Click on the Title of your Multi-User migration
Click on the Quick Action button and select Edit Migration Plan
You will then see the full list of users.
Using the Filters and Security Migraion buttons you may change the filters or security options (for supported systems) for the specific user you have chosen