Clans will be matched up based on the overall strength of its members. Strength is based on each member’s attacking power (troops, army camp capacity and spells) and defensive power (defense buildings, walls and traps). Heroes constitute towards a player's offensive and defensive power.
Unlike the Multiplayer mode, trophies do not factor in when clans are matched. Town Hall levels aren't a deciding factor in matchmaking either. Only once a player has built the defenses unlocked at his Town Hall level and upgraded to the new troop levels does his weight begin to increase. Therefore the presentation of Town Halls in the Battle Map (whether they are above or below your level) can't be taken as an accurate representation of the opposing team's strength.
Matchmaking aims to match Clans with similar ratios of offensive and defensive power against each other. Matchmaking will always try to find matches within a tolerable time however, causing variety in the quality of matchups.
Different layouts and base designs do not affect strength. The only way a member’s strength can be changed is if they upgrade their troops, defenses, spells, etc.
Finally, matchmaking will factor in Win/Loss records. This ensures that your opponents are worthy adversaries.