Muahmmad - do you know what the minimum number of rows are in each file? If so, then you could create a vector of integers, one for each file, where the sum of all elements in the vector is 100000 (the number of rows that you want to extract). You can initialize the vector to that of all ones
numFiles = 29000;
selRowsPerFile = ones(numFiles,1);
so that at least one row is selected from each file.
There may be some code on the MATLAB File Exchange that can create this vector for you (subject to the constraint of each element in the vector being at least one, and the sum of the elements in the vector being exactly 100000). If not, then you could write a simple while loop with randi to randomly select more rows for each file, until the 100000 rows have been assigned.
Then, once you have your list of files, for each file you can use xlsread to read in the data and then randomly selected a number of rows (again using randi) from that data (using the selRowsPerFile vector to tell you how many rows to read). Once those rows have been selected, then use xlswrite to write the data to file.
