You don't give any data nor attach a plot to see the issue specifically, but you set fixed axes limits on log axes the same way as you do for linear ones--use ylim (or set for low-level control or in conjunction with other properties on the axes in one call).
Simple example--
y=[10*rand(10,1), 1E5*rand(10,1)];
hAx=semilogy(y);
ylim([1,1E6])
ylim([.5,4E5])
Salt to suit for your particular case...
