Hi @sajjad.sarikhan,
If I understand correctly what you're trying to do, you should provide the --p-min-frequency parameter to achieve this.
Here's an example using the table.qza file from the Moving Pictures tutorial. You can see from the feature table summary that the median feature frequency is 25. The feature frequencies presented in this summary are the total number of times each feature was observed across all of the samples, which as I understand it, is what you want to filter based on.
I can filter that table retain only features that have a frequency of at least 25 as follows:
qiime feature-table filter-features --i-table table.qza --o-filtered-table table-mc25.qza --p-min-frequency 25
If I then summarize that table, I can see that the minimum feature frequency is now 25 (here's a screenshot of the feature table summary that I created locally with the command qiime feature-table summarize --i-table table-mc25.qza --o-visualization table-mc25.qzv):
Does that get you the information you're looking for?