The present invention discloses devices and methods for creating multiple lesions using ablation devices in anatomical regions such as the heart, for example to treat cardiac arrhythmias. The present invention discloses methods and devices to create continuous lesions using area ablation devices. The present invention discloses various embodiments of reference assemblies for accurately positioning ablation devices having ablating portions, especially deployable ablation portions adapted for area ablation. The ablation devices are positioned using the reference assemblies in the anatomy to create one or more lesions. The present invention also discloses several method embodiments for creating continuous lesions using deployable ablating portions to produce two or more overlapping lesions.