using ubuntu to remove malware

[brown sugar]

Whenever I suspect that my flash drive has been infected what I generally do is, boot my system in Ubuntu, plug the flash drive, look out for suspicious files and delete them. This route has been fail safe for me. If there is a .exe file I open them using gedit and if I feel that it looks weird I delete it right away.
However, a friend recently reported that he encountered a problem in this method. His drive was infected. All the folders present in the drive disappeared and was replaced with a single file that cannot be opened. He tried opening it in Unix but couldn't. (!!) The same situation persisted. A single file that an't be opened. He's not sure of the file type. But can this really happen? I believe .exe , .inf , .bat files  are incapable of running on ubuntu. Clarification required.

OS Info : Windows7/ubuntu 12.04 dual boot

[brown sugar]

He approached a data recovery center. They were unable to recover the data either. Only images were retrieved. (the drive contained docs and ppts.. the images were actually a part of the docs) They have formatted the drive and have written the recovered data on top of it. My question : is it possible to retrieve the original docs and ppts now?

[SuperDave]

Here is a link where you download some safe recovery tools.

[brown sugar]

Thank you superdave. But your post doesn't answer my question. Stellar Phoenix, recuva and various other softwares were tried to recover the data but to no avail.

My questions :
1. can you name some companies/organisations who can restore the data professionally? (I'm looking for ones like Kroll Ontrack)
2. The infected pendrive has been formatted and filled with the PARTIALLY recovered data (only images). Is it still possible to try and recover the original data(docs and ppts)?
3. What could be the possible reasons for the partial recovery?
4. Are there malware that can work on both Windows AND Ubuntu?

PS sorry for my late reply. Was caught up in several stuff.

[SuperDave]

can you name some companies/organisations who can restore the data professionally? (I'm looking for ones like Kroll Ontrack)

Sorry, no.

The infected pendrive has been formatted and filled with the PARTIALLY recovered data (only images). Is it still possible to try and recover the original data(docs and ppts)?

If it has been reformatted they're probably gone.

What could be the possible reasons for the partial recovery?

I can't say since I wasn't there.

Are there malware that can work on both Windows AND Ubuntu?

Hackers don't usually create malware for OS's like Ubuntu or Apple because they are not that popular.

[brown sugar]

Thank you for previous post. I still require some clarifications.

1. you can't name them because there aren't any or is it because of the forum restrictions? (Trust me I have googled for such centers but having a tough time finding any reliable sources)
2. I've heard of 'data restoration' wherein people try to recover data from burnt/damaged hard disks. And that, eventhough a disk has been reformatted, it is still possible to recover the data. Is it applicable only to hard disks and not flash drives?

Additional Question : Is my method of using ubuntu to delete suspicious looking files from my affected flash drive, potentially dangerous?

[SuperDave]

2. I've heard of 'data restoration' wherein people try to recover data from burnt/damaged hard disks. And that, eventhough a disk has been reformatted, it is still possible to recover the data. Is it applicable only to hard disks and not flash drives?

Yes, it's possible. Please read this.

Is my method of using ubuntu to delete suspicious looking files from my affected flash drive, potentially dangerous?

It's not a very good method of cleaning a computer since you don't know the function of the files you are deleting.