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The majority of top film programs are regulated to the Los Angeles and New York City areas, mainly because that is where the industry was born and where the oldest programs are. This does not, however, define the only location that you can get a top notch film education. There are few great film schools programs in the United States, but only about half of them are in Los Angeles or New York City.
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Rochester Institute of Technology's School of Film and Animation
The Rochester Institute of Technology's School of Film and Animation is located in the upstate New York town of Rochester, which sits in the middle between small and medium sized cities. The program itself is nestled at one of the top technical schools in the country, and houses many of the top art programs. The film program itself has been listed in the top fourteen film graduate programs by U.S. News and World Reports, and its undergraduate program is also considered top of the line.
The program itself is based around a three project system where you focus on a one quarter project your first year, a two quarter project your second, and then a full year for your thesis film. Beyond that you will produce a number of other smaller project, focus in on all of the production and post-production skills and technologies, and really dial in to producer and writing work.
RIT has a good record for industry professionalism, though not as good of an alumni list for high profile filmmakers. RIT stands out as a great choice if you want to be technology focused, connected with animation at all levels, and want to dig into the pool of undergraduate talent. You will have the ability to focus on a parallel between proficiency in a skilled area like post-production or cinematography while also working on your portfolio and ability as a full filmmaker. RIT is a high level private school and the tuition costs reflect this, but they tend to be liberal with scholarships and the living costs in Rochester are on the lower end of the spectrum nationally.
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Florida State University
The Florida State University College of Motion Picture Arts' Master's of Fine Arts program is considered one of the very top in the country. The program itself has a firm grounding in the technical aspects of filmmaking that most directors are going to need, and since they also have a screenwriting Master's of Fine Arts you can get a nice parallel focus in production and writing. There is also the opportunity to specialize in certain areas of production at FSU, which is unusual for many film graduate programs. FSU is also known for the Torchlight Program that allows for industry professionals to really interact with the student body.
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University of Texas - Austin
University of Texas - Austin dominates the lower middle of the U.S. in terms of graduate programs. Their graduate film department is housed within their journalism and media section that gives its own certain types of benefits. This allows you to really tap into broadcast journalism and documentary filmmaking for a different type of film experience. UT - Austin still rounds out in the top ten list set up by U.S. News and World Reports, which puts it in a unique position where it stands out as one of the most important film graduate programs with other periphery fields that you can jump into. Through this the MFA in Film & Media Production puts you into both documentary and narrative film equally and takes the three year program as a three step process to developing skills. There is a higher premium on media studies placed in this MFA program and slightly less technical focus, but that can be appropriate for some people's educational goals.
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Northwestern University also houses their film program in the School of Communication in a sub-section call Radio, Television + Film. Northwestern is notable in the way that it includes an MFA in Writing for the Screen and Stage, but not one strictly on film production. They do have a notable undergraduate program, so the available coursework is there so that you can integrate this into the writing focused MFA so that you can double dip. For a great school in a strange part of Illinois this is an interesting choice.