This tutorial is based on BlueStacks App Player for Windows v 0.9.0.4049.
1) Look for the Settings App in All Apps.
2) Click / Tap on the Settings app to open it.
3) Click on "Manage Applications" as shown below.
4) Select the app(s) you wish to uninstall, e.g, whatsApp and Click / Tap on "Delete".
5) Click "Continue" to delete.
6) Now, click "Done". App(s) will be deleted from BlueStacks.