srinija - the variable popupmenu2value is local to the popupmenu2_Callback function only and so is not accessible from the pushbutton1_Callback function. If you want to use that value in the pushbutton callback then you can just determine it as you are doing already in the other callback. Try
function pushbutton1_Callback(hObject, eventdata, handles)
contents1=get(handles.popupmenu2, 'String');
popupmenu2value=contents1{get(handles.popupmenu2, 'Value')};
fismat=readfis('oralcancer_rulebase.fis');
% etc.
But then you will have the same problem with all the other variables that you are trying to use that haven't been defined in your pushbutton callback
out=evalfis([popupmenu2value popupmenu3value popupmenu4value num smokingvalue alcoholvalue gendervalue tumorsitevalue],fismat);
You will need to define these variables within the pushbutton callback if you wish to make use of them (or save them to the handles structure in the other callbacks and then access them here through the struct).
