You have two methods to choose from.
1 - Clip brushes
Make a brush and give it the clip texture. The player will not be able to pass through this brush, and they will not be able to see it.
One bad way of making a ladder is to make a detailed ladder as a func_illusionary. Inside the ladder make a set of steps that are 1 unit wide, and put it inside the ladder. When the player walks into the ladder they are instantly transported up the invisible staircase (just like a normal staircase, but all of the steps are within boundaries of the ladder's space, so the player moves upwards).
2 - Skip Texture
Make a brush and create a texture with the name 'skip'. Apply the texture to the brush. The brush will still be there, but it wont be drawn. You can use this tool on individual faces too. And you can apply it to brush entities, like doors for example. This can be used to do all sorts of things in Quake.
When you compile the map, you have to run the newskip tool to remove the faces. Created by Metlslime:
http://www.celephais.net/files/newskip.zip