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I am not an EU citizen and currently I am doing a PhD in Switzerland possessing a B permit. I plan to terminate my contract and start PhD anew in Prague (3+ years). As I understood my B permit will be cancelled after termination of my PhD in Switzerland. Should I apply for a student visa, or directly apply for a long-term residence permit?

I am afraid to have a situation when I apply for a student permit, which by some random missing paper may be declined after 2 months and then a new application for long-term permit and/or student permit will result in an extra two month waiting time period, while I am allowed to stay in Czech republic only 90 days after arrival to the country. So, I can easily exceed that 3 month limit which will result in troubles.

closed as off-topic by David Richerby, CMaster, mts, Berwyn, blackbird Aug 2 '16 at 12:24

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    Does the University in Prague not have an international office? If you are about to start there, they should be able to guide you through the process. – DCTLib Aug 2 '16 at 12:03
  • They said me that foreigners are taking care of coming by themselves and they don't know how it works. – hrexen Aug 2 '16 at 12:11
  • Your question is better suited for expats and should soon be moved there but if there is no international office / secretary / colleagues or other staff to help you, this does not sound well for your institution IMHO. – mts Aug 2 '16 at 12:14
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    Czech universities are extremely incompetent when it comes to visa questions. Move your question to Expats. SE and I'll answer it there. – JonathanReez Aug 2 '16 at 12:37