Works like any other guild system. You can assign sub-leaders to invite players. Last I played, max amount of people a guild can hold is 100.
You create a guild by purchasing a clan permit for the city of your choice. Initially only Third Home and Shinjuku Babel are available. Once Souhouzan and Arcadia are accessible, you can purchase permits for there too. The only benefit I know of from making either Souhouzan or Arcadia your base is that each guild member can recieve a free warp stone once every 24 hours.
In order to join a guild, you either need a leader or sub-leader to invite manually (by right-clicking you and inviting you from the menu), or you can do a search on the terminal of the guild's home base and send an application. Leaders and sub-leaders can view the applications from either the Community menu. I believe there is a fee to post an advertisement for your guild on the terminal (or to place your guild's ad back to the top of the list).
I believe there was an update sometime last spring or winter that improved the guild system. The only feature I've noticed is that guilds can now assign an emblem that goes beside their name. That and I believe you can now increase your guild's level. How or what for, I have no clue.