Unable to boot to Windows 7 due to Virus

HP Probook - Windows 7 - Virus Issue Virus attack replicated AVG Virus software and said to quarantine and reboot which seem to have enabled virus to affect in major way. Initially it gave windows but blocked access to all files then unable to Boot windows 7 at all Downloaded Kaspersky Boot Disk and am able to access all files using the other OS - but want to restore factory settings... all partitions appear to have been deleted. Other than copying all files I want to keep to an external HD and restoring factory settings (which I dont even know will work) is there any other options?

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