Some maps have world brushes that only show up in one gametype. As an example, play mp_shop on DM and INF. You'll notice that the helicopter is not present in DM. mp_col1 provides and even more striking example: the entire pyramid structure at the Blue Team spawn location in INF is missing in CTF and other modes. More "down-to-earth" examples are the pads for the CTF flags, which are only present in CTF mode.
This is actually achived in a rather simple manner. In Radiant, select the brush you wish to show up in only a specific mode. Right-click the workspace to bring up the entity list, and select "func_static" to change the brush to a "func_static" entity. Then, with all of the func_static entities selected, press "N" to bring up the entity preferences window. Add a "gametype" key specifying the gametypes you wish the brush to show up in. For instance, if I wanted a tower to show up only in INF and CTF, I'd add the key:
"gametype" "inf ctf"
...to all "func_static" brush entities for that tower.
The process is actually slightly easier for glass and windows, since they're already entities. Simply select the glass\window entity, bring up the entity preferences with "N" and add in the "gametype" key as specified above. Viola! Now you have some world structures that only show up in the gametypes you specified!