Method 1:(tried)

You can use GParted tool in elementary to achieve what you want. This is not provided by default. To install it type this in your terminal:

sudo apt-get install gparted  

Steps to make ntfs partitions hidden:

1. Open gparted from slingshot menu
2. Right-Click on desired ntfs partitions
3. Goto Manage Flags
4. Check hidden flag
5. Log in and out or Restart

Remember to unmount the partition first.

Method 2:

Whichever filesystem you mount gets mounted to /media. In-order to hide it from pantheon files and nautilus, you need to mount it anywhere else than /media, optimal choice would be to mount it under /mnt.

Following is the link which describes how to do it in nautilus, it should be similar for pantheon files as elementary is a derivative of Ubuntu.(didn't try this for myself)

Link: hide ntfs partition in ubuntu nautilus (check the second and third answer, first answer uses disk utility in ubuntu)

Method 1:(tried)

You can use GParted tool in elementary to achieve what you want. This is not provided by default. To install it type this in your terminal:

sudo apt-get install gparted  

Steps to make ntfs partitions hidden:

1. Open gparted from slingshot menu
2. Right-Click on desired ntfs partitions
3. Goto Manage Flags
4. Check hidden flag
5. Log in and out or Restart

Remember to unmount the partition first.

Method 2:

Whichever filesystem you mount gets mounted to /media. In-order to hide it from pantheon files and nautilus, you need to mount it anywhere else than /media, optimal choice would be to mount it under /mnt.

Following is the link which describes how to do it in nautilus, it should be similar for pantheon files as elementary is a derivative of Ubuntu.(didn't try this for myself)

Link: hide ntfs partition in ubuntu nautilus (check the second and third answer, first answer uses disk utility in ubuntu)