Thank you so much Rudiger I able to change to nonindexed data color to black. For future reference to other people who looking to change colors
To change notIndex data color
1. Go to phaseList.m line 221
2. change c = ones(1,3);(white notindexed data) to c = zeros(1,3); (black notindexed data)
To change EBSD phase color
1. go to mtex_setting.m line 114 (EBSD Phase Colors)
2. change EBSDColorNames and its corresponding EBSDColors
If you want to change phase color form command line
ebsd('iron').color=[1 0 0]
Zelda