To set set negative values in a certain column of matrix "A" to 0, you can do this:
For this example we assume A is a 2-D number matrix and that we are getting rid of negative values in the 2nd column.
>>A(:,2) = max( A(:,2), 0 )
This line of code replaces each negative number in the second collumn with 0. Each positive number in the second collumn will stay the same.