I am not certain exactly what you want.
One of these should work:
x1 = 0.0001;
x2 = 0.001;
y1 = round(x1)
y2 = round(x2)
roundn = @(x,n) round(x*10.^n)./(10.^n);
z1 = roundn(x1,3)
z2 = roundn(x2,3)
The built-in MATLAB round function rounds to the nearest integer. In R2015a, you can also have it round to a specific number of decimal places, but if you have an earlier version, my ‘roundn’ anonymous function will do the same thing.
Run my code snippet here to find out which of them does what you want.