From your question what I understood is,
- App need to store pdf file securely.
- Use internal storage as preference.
1. Use secure encryption/decryption algorithms like AES-256 with password based cryptographic key.
Also code obfuscation & jumble algorithms can be applied for secure key generation to avoid reverse engineering attacks upto a level.
2. For Internal storage of application you can change android:installLocation="internalOnly" in manifest file
<manifest xmlns:android="http://schemas.android.com/apk/res/android"
package="string"
android:sharedUserId="string"
android:sharedUserLabel="string resource"
android:versionCode="integer"
android:versionName="string"
android:installLocation="internalOnly">
. . .
</manifest>
For more info please refer this question & answer