A common issue being reported by Microsoft WebMatrix Beta users, is that they are unable to easily delete a SQL Server Compact Edition database from with WebMatrix itself. There is a way to delete the CE databases using the Files workspace of WebMatrix, read on to see how.
Let’s start by Getting a site set up to work with.
Step 1: Open the Microsoft WebMatrix Beta
Step 2: Select choose site from template

Step 3: Select the “Empty Site” and click “ok”

Step 4: Navigate to Databases Workspace by clicking the Databases button in the lower left hand corner of the screen.

Step 5: Click the "New Database" button in the ribbon.

When you click 'New Database' WebMatrix creates an empty SQL CE database underneath the App_Data folder. WebMatrix then adds a dynamic connection to the database file under the site node in the Databases workspace.
Now that we now have a database listed underneath the 'Empty Site' node in the tree, let's look at how to delete it.
Step1: Navigate to Files Workspace by clicking the Files button in the lower left hand corner of the screen.
Step 2: Expand the folder structure until the App_Data folder is expanded
Step 3: Right click the 'Empty Site.sdf' file and select the Delete option.
Step 4: Navigate back to the Databases workspace, the refresh the 'Empty Site' folder.
You have now deleted your file based SQL Server Compact Edition database connection from the databases workspace of your application.