You can access the individual lines in the axes if you wish (and you can set their Color property to [0 0 0]).
Here is an example of how to remove the lines from a simple boxplot using this method:
load carsmall
figure;
boxplot(MPG, 'ExtremeMode', 'compress');
xlabel('All Vehicles')
ylabel('Miles per Gallon (MPG)')
title('Miles per Gallon for All Vehicles')
fig = figure;
boxplot(MPG, 'ExtremeMode', 'compress');
xlabel('All Vehicles')
ylabel('Miles per Gallon (MPG)')
title('Miles per Gallon for All Vehicles')
lines = fig.Children.Children.Children
lines(4).Color = [1 1 1];
lines(5).Color = [1 1 1];
lines(6).Color = [1 1 1];
lines(7).Color = [1 1 1];
