You're right, Android M or Samsung or iPhone APIs only allow to verify current user against user of device.
With Android M or Samsung or iPhone APIs you can't get fingerprint template or image.
As @ianhanniballake the only solution is to create a user in Android for each employee. But each employee need to select is user and after, he could be authenticated.
There's some fingerprint scanners compatible with Android Platform and with SDK for Android. These SDKs allow to get fingerprint image or template. Scanners are plugged on USB port so you can't charge tablet and use fingerprint scanner simultaneous. For instance:
- http://www.dermalog.com/en/products_solutions/fingerprintscanner/
- http://www.futronic-tech.com/product_fs80h.html
- http://www.crossmatch.com/authentication-hardware/
There's also some devices with integrated fingerprint scanner and with SDK to get fingerprint image or template.
To match fingerprint, some SDK have matcher but if you have lot of user you should use an AFIS solution.