I have a 4 GB thumb drive that I cannot use to make Netbook Remix because it has a partition with a read-only file system and some propietary software in there.
If loading the remix in the read-write partition I get error: Invalid system disk.
I need to nuke this drive, fill it with zeros first and then reformat.
Unable to delete partition or reformat now.
Standard Linux utilities like gparted or Parted Magic don't work on this drive, neither does the CLI.
There are utilities out there but those nuke the hard drive.
I need something that will selectively nuke this thumb drive.
Thanks in advance.

Need more information on the flash drive.
If it is a Sandisk U3 type flash drive you will need to go to their website and download the removal utility. This is a windows only application and AFAIK nothing else will work.

Welcome To LinuxQuestions.

It is PQI, sorry cannot give more info at present, don't have the drive with me.

PQI does make U3 drives so I my first SWAG it is the cause of your problems. As stated you can download a U3 removal tool but it is a windows application.

Thanks for answer.
In fact the whole model name is Cool Drive U350.
No problem installing a Windows app., until open source can build things like Flash CS4 I am stuck with it for some things.
I will also send a support ticket to PQI, will post resolution here, if any.

http://www.pqigroup.com/upload/download/Dr.UFD.zip
The response from PQI support sent me to this utility, it is in fact a Windows utility, but it did the job.
Please note that U3 removal tool from Sandisk didn't work.
Thanks so much for pointing me in the right direction.

Your Welcome

I have been unable to remove this malware. I hope this will be of help to some one. I finally obtained what I think is a honest answer to the U3 malware. It is a proprietary drive partition that is only removed with SanDisks software. That is probably why no one has been able to remove it from Linux. Whats odd is there removal software went from something like 1.8 MB to 2.2 MB and now its at 3.3 MB. Why the constant increase in size and such a large piece of software to just do this one thing? One of the support people at SanDisk said MS was behind it. Another support person at SanDisk said it was a piece of hardware on the USB thumb drive. Support people will feed you anything at times to get you off the phone.

You can use dd to wipe the drive. If the drive comes up as /dev/sdb, then run 'dd if=/dev/zero of=/dev/sdb bs=1 count=5G'.

Then use gparted to put a fresh partition back on it.

CAUTION: Backup your data and get the device names correct or lose data.