Upload Mp3/Database files from PEN DRIVE to SD CARD problem with speed
There are so many variable involved that you have not given sufficient information for outsiders to give complete and/or valid tips. 

Lets start with some simple math considering the maximum throughput of USB full (around 1 MB/s) and an average MP3 file size of 3.5 MB :

2000 files * 3.5 MB/file / 1 MB/s = 7000 s = 117 min


With 10 kb:

2000 files * 0.01 MB/file / 1 MB/s = 20 s


So already, depending on the actual use case, you may or may not be USB limited and we cant tell you which without more data. Another issue is that saturating the USB and doing other meaningful tasks such as managing a file system and sending the data back out the SPI may not be possible with simple purely procedural MCU code if your not running at maximum clock speed. You will likely need to use DMA transfers to keep your buffers flowing while you manage the file system on the CPU. If your software is not a bottleneck, your MCU does support USB High speed which definitely could not saturate before software or the SPI does.