Point #3 was confusing, but this is what it should look like. In this case, I've plotted the X, Y, and Z variables on three separate plots because of the ambiguity of point 3. If you are looking to have a legend with all 1000 files in it, you will not like the result. Again, this could be me misunderstanding your question. If that is the case, please clarify.
[file,path,indx] = uigetfile('.xlsx','MultiSelect','on');
if indx == 0; error('No file selected'); end %nothing selected
cd(path) %change directory
if ~iscell(file); file = {file}; end %if you only select one file
fig1 = figure;
ax1 = uiaxes(fig1);
hold(ax1,'on')
fig2 = figure;
ax2 = uiaxes(fig2);
hold(ax2,'on')
fig3 = figure;
ax3 = uiaxes(fig3);
hold(ax3,'on')
for x = 1:length(file)
fileData = readtable(string(file(x)));
plot(ax1,fileData.X,'o') %plotting just X data
plot(ax2,fileData.Y,'o') %plotting just Y data
plot(ax3,fileData.Z,'o') %plotting just Z data
end
hold(ax1,'off')
hold(ax2,'off')
hold(ax3,'off')
legend(ax1,extractBefore(file,'.'))
legend(ax2,extractBefore(file,'.'))
legend(ax3,extractBefore(file,'.'))
