If you mean basic letters, then e.g.
idx = randi( numel( yourCharArray ), 1000, 1 );
replacementChars = char( randi( 26, 1000, 1 ) + 96 );
yourCharArray( idx ) = replacementChars;
would replace them with lower case letters from 'a' to 'z'.
If you want other characters then you can change the hard-coded 26 and 96 there as appropriate to index into the ascii character set. 26 obviously represents the 26 letters of the alphabet and 'a' is represented by ascii 97. The random integers will be created from 1 to 26 to add to this.
If you want to you can be fussier to ensure that all your 1000 indices are unique also, but I shall leave that for you.