This is definitely possible, although not as direct as you may prefer (we've found that not many people are still using Present/Absent calls with MAS5--they are instead filtering by minimum intensity).

You want to first generate the present/absent calls using the Microarray Menu | Affymetrix | Generate Affymetrix MAS5 Report (Tools Menu | Affymetrix.. in version 3.6 and later).  Choose your CEL files again, but make sure to select the Generate detection data (you can unselect the other options if you want).  DO NOT SELECT Report p-values, as this will override the generation of the detection data. 

This will generate a new dataset, called MAS5Detection.  This dataset shows a 0 for present, 1, for marginal, and 2 for absent.  You can use the Filter command in the Microarray menu to filter the variables.

To filter variables where at least 25% of the calls are present, you would change the Criterion to "Quantiles" and set it "= 0". Then click Add Criterion. Then, at the bottom of the screen change the Quantiles section to 25%.  You can test out how many variables pass by clicking the Test button.  When you are ready (after changing the quantiles section to a number you are happy with), click Submit.  This will generate a List of variables that passed your criteria.  You can use this list for subsetting, filtering, etc..