Preventative measures should always be taken to protect new crops, vegetable gardens, and plants that are placed into a chipmunk habitat. Similar to the woodchuck, the chipmunk is primarily a surface forager, however unlike the woodchuck, fencing is not an effective deterrent against the chipmunk because it is such an agile climber.
Preventative measures involving exclusion and habitat removal are typically the only measures necessary to prevent any sort of chipmunk problems. Remove piled debris and unkempt shrubbery from areas where chipmunk control is desired. Removal of these items will eliminate concealed areas where the chipmunk may hide or build a burrow.
Use ¼" hardware fabric (wire mesh), or some other sort of barricade, to cover any holes that may allow passage into buildings. All holes should be covered; it is amazing how small of a hole these animals can squeeze through.
In areas where seed planting has become a problem due to chipmunk excavation and consumption, installation of a layer of ¼" hardware fabric over planted seeds is recommended. Place seeds, roll over with fabric, and bury with soil. It is important to extend the hardware fabric 12-inches beyond the planted area on all sides to prevent access from the edge.
Place any source of food: pet, bird, livestock, etc, at least 20 to 30 feet from any structure to eliminate the creation of an ideal food/shelter situation where the chipmunk might find it easy to eat and hide or eat and burrow.