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Base model is available but is a small box at the bottom of the "build your IS" option packages page. It appears as if Lexus does not want to sell them that way.
Base 350 has no Nav, no premium sound, no memory seats, has 17" wheels, Nuluxe, etc. You can always order it but expect a long wait.
This.
The Lexus online configurator sucks. You can indeed get a IS350 with no options, but it would have to be a factory order. You can also get an IS350 with only Park Assist for example, but that is something the online configurator will not show you.
It seems every few days the lexus.com configurator cleans up a little more. Right now it's pretty rough. They will clean it up as we move forward I'm sure.