You can do that by two ways. One is by a function or other by SQL query.
In your function just get all the posts having post_type = <your-custom-post-type> and delete those . Just add that function to theme init method.
You can also do that through just SQL query. Query may be like below.
SELECT * FROM wp_posts WHERE post_type=<your-custom-post_type>
If your are non-technical then second options will be best for your.
Note: Before doing any thing just backup your database for your safety, if any thing goes wrong, you can directly replace the dump.