This is a comparison that has been done countless times. There are hundreds of articles offering different points of view on similarities and differences. The short answer is: yes. Japanese Americans were rounded up and forced into internment camps. Anti-Japanese propaganda about invasion in the style of the time was prevalent.

Of course the specifics differ. Japan was a sovereign nation, al-Qaeda was a non-state actor. At Pearl Harbour the casualties were mostly military, whereas the Twin Towers deaths were almost entirely civilian.

I'd suggest some further reading. There's plenty out there - and it's the sort of well-covered issue that you could really form you own view on.