It sounds like your USB disk is formatted using a GUID partition table (GPT); the EFI partition a standard part of how OS X formats disks with GPT, so it probably shouldn't be removed. What I suspect you really want, though, is to replace the GPT with a master boot record (MBR) partition table instead.
To change this on OS X, you need to reformat (erase) the disk using Disk Utility. In its sidebar, select the disk. Make sure you select the disk device entry, not the volume; the volume will be indented below the disk's entry in the sidebar. Info about the selected disk will be listed at the bottom of the Disk Utility window, including the partition scheme. If it GUID Partition Table (or GUID Partition Map), you need to erase the disk. If it says Master Boot Record, something weird is going on because the EFI partition shouldn't exist under that. If it says something about MS-DOS or Windows, you have the volume selected instead of the disk; try again.
Assuming this is the problem, you can erase the disk (again, make sure you have the disk, not the volume selected; also that it's the right disk!). There'll be a "Format" pop-up menu: choose "MS-DOS (FAT)". If you're using El Capitan, there'll also be a "Scheme" pop-up menu: choose "Master Boot Record" (older versions assume this automatically based on the MS-DOS choice). That should get you a disk with a single FAT32 volume, with no EFI partition.
Note that if you erase just the volume, not the entire disk device, it'll leave the partition scheme alone, and the hidden EFI partition will still be there. You must erase the entire disk!