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The current network setup is like this: Company A has a network setup consisting of Cisco devices only. It has an FTP server where all files are stored and accessed. Company B has a different setup from A (no networking devices, only a wifi modem), and is in need of certain files from A.

According to http://www.deskshare.com/resources/articles/ftp-how-to.aspx, you can upload and download files after installing a client software and providing an address, username and password. But is this only applicable to clients within Comapany A or is it also applicable for clients of Company B too?

Also, how does an FTP server work with VPN in this situation?

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Start at the end: A VPN places the client computer on the host's network, or at least one of them. Once you're connected to a VPN, you're on the host's internal network and no longer have to worry about the network configuration; all services should just work as usual. Even when placing VPNers on a DMZ, the DMZ should be all configured to handle inbound requests with lower security than the edge firewall.

As for the main question, that's all part of the firewall configuration. You can allow it through, restrict it completely, or allow it only on specific ports or from specific IPs. Deep packet firewalls can even dynamically block connections that seem abusive. In order to open FTP at all, you have to forward port 21 (by default) to the FTP server, as well as a small range of ports for the second connection -- these can be any ports you want, you get to define them on the FTP server. You configure the FTP server with the correct external IP, because it has to tell the client where to connect, and then everything will work. Active mode, in which the server connects back to the client, is rarely used because of NAT and firewalls these days.

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