Sounds like you're mounting CS:S content. Check your /cfg/mount.cfg file... you'll see something like this..
"mountcfg"
{
"cstrike" /home/steam/content/css/cstrike
}
You can rem out (//) the cstrike entry if you want. However, it's entirely possible that you in fact >want< to mount CSS content to support various CSS props/models, etc that you're running that rely on CSS content. If that's the case, then yes... you'll need to edit the mapvote system you're using to expressly blacklist the maps you don't want available for vote.
If you are using a fretta-based prophunt, then the map list is built/handled in sv_gmchanger.lua. You'd edit the following to have it ignore maps you didn't care about (ie, not add them to AllMaps if they match a specific set of strings or pattern).
local AllMaps = file.Find( "maps/*.bsp", "GAME" )
for key, map in pairs( AllMaps ) do
AllMaps[ key ] = string.gsub( map, ".bsp", "" )
end