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There is an airside transit bus between T3 and T2, so you can transfer between your Emirates and flydubai flights without passing immigration or requiring a transit visa. The bus leaves from Concourse A apron level. Any Emirates staff in terminal 3 can help you find it if necessary.
If you didn't happen to arrive at an A gate, there are also airside buses that will take you to concourse A.
If you would like to leave the airport during your layover, you can apply for a transit visa via Emirates by going to Manage your booking.