As the jalapenos smoke, they will start to turn almost black and dry up becoming leathery to the touch. Depending on how long you smoke the jalapenos, they may be nearly done or need more time to completely dry. You want the chipotles dry so that they will last without loosing their flavor. Chipotles that are not completely dry will lose the smoky flavor over time and will need to be refrigerated or frozen to preserve them.
There are a few options to finish the drying process. If you live in a warm, dry climate, you can lay them out in the sun. Place them on screens to allow airflow around the chipotles.
You can use a food dehydrator to dry your chilies. There is one draw back to this though. The smokiness of the chipotles will soak into the surfaces of the dehydrator, leaving it with a smoky flavor for days, or even months.
Lastly, you can finish off the chipotles in the oven. This will release a smoky aroma into your house for a day or two, but it won’t be too bad. Set your oven to a very low temperature (below 200 degrees F) and spread the chipotles out on baking racks. Don’t place them on a cookie sheet or pan, as this will impede the drying process.
Dry chipotles until they are completely brittle.