One way that I have seen used to protect data on a hard drive could also be used on a flash disk.
First of all the data is encrypted, using whatever encryption tool you are most familiar with.
Second, the disk should be prepared for writing, either by formatting it with the default FAT system used for most flash drives, or by using a cryptographic file system.
Third, the encrypted data is written to the disk/drive.
Finally, erase the partition table of the disk/drive, if the FAT formatting is used.
This will cause the device to appear as unformatted to most systems so that the data cannot be seen by the host OS. If the cryptographic file system is used, unless the host OS has drivers to read that file system, it cannot see the files you have placed on it.
This provides security from programs designed to scan flash drives when they are plugged in.
Using a simple tool like rescuedd, the files can easily be found and unencrypted when they are again needed, and connected to a trusted system.