[{"_id":1,"customers":[{"key1":"val1","key2":"val2","subkey":{"subkey1":{"subkey2":"subval2","subkey3":"subval3"}}},{"key1":"val1","key2":"val2","subkey":{"subkey1":{"subkey2":"subval2","subkey3":"subval3"}}},{"key1":"val1","key2":"val2","subkey":{"subkey1":{"subkey2":"subval2","subkey3":"subval3"}}},{"key1":"val1","key2":"val2","subkey":{"subkey1":{"subkey2":"subval2","subkey3":"subval3"}}},]},{"_id":2,"customers":[{"key1":"val1","key2":"val2","subkey":{"subkey1":{"subkey2":"subval2","subkey3":"subval3"}}},{"key1":"val1","key2":"val2","subkey":{"subkey1":{"subkey2":"subval2","subkey3":"subval3"}}},]},{"_id":3,"customers":[{"key1":"val1","key2":"val2","subkey":{"subkey1":{"subkey2":"subval2","subkey3":"subval3"}}},]}]

db.collection.update({},{$set:{"customers.$[].subkey.subkey1.subkey2":"new_subval2","customers.$[].subkey.subkey1.subkey3":"new_subval3"}},{multi:true})