When you do allchild(figList(iOld)), you are copying everything. That includes the uicontrols and menu. That is the source of the error. If you only want to copy the graphics objects, you could do as follows (will copy only the 'axes' objects):
for ii = 1:10
plot(rand(10,1));
end
% Get a list of all existing figures
figList = sort(get(0,'Children'));
for iOld = 1:length(figList)
figOld = figList(iOld); % This is a figure to replace
% Used later to make sure size of figure is correct
posOld = get(figOld, 'pos');
figNew = figure; % Make new figure
% Used later to make figure appear at
% default horizontal position on screen
posNew = get(figNew, 'pos');
% Copy over lines (but not formatting)
%Copy only the axes %This is the new bit
kids = allchild(figList(iOld));
type = get(kids,'Type');
idx = strcmp(type,'axes');
copyobj(kids(idx),figNew);
% Reproduce figure name and size however don't move it horizontally
set(figNew, 'Name', get(figOld, 'Name'), ...
'pos', [posNew(1:2) posOld(3:4)]);
% Get rid of old figure
close(figList(iOld));
end
