You forgot to attach your table so I had to create one.
% Create table data because OP forgot to attach his.
v1 = rand(100, 1);
v2 = rand(100, 1);
v1(1:10) = -9999;
v1(end-4:end) = -9999;
v2(1:15) = -9999;
v2(end-14:end) = -9999;
t = table(v1, v2, 'VariableNames', {'Column1', 'Column2'})
% METHOD 1: uSING table2array()
variableNames = t.Properties.VariableNames;
m = table2array(t);
m(m==-9999) = nan;
tFixed = table(m(:, 1), m(:, 2), 'VariableNames', {'Column1', 'Column2'});
% METHOD 2: USING FOR LOOP
% Now we have our table and we can begin replacing -9999 with NaN.
for col = 1 : width(t)
map9999 = t{:, col} == -9999;
t{map9999, col} = nan;
end
