You can use net.sf.jasperreports.export.{format}.exclude.origin.{suffix}.{arbitrary_name}(see the http://jasperreports.sourceforge.net/config.reference.html page for details) property for excluding bands (Page Header and Page Footer in your case) for exporter.
The sample:
The input data, csv file (datasource):
AAA,US,XXXXX
BBB,UK,XXXXX
CCC,ID,XXXXX
DDD,CC,XXXXX
EEE,SA,XXXXX
FFF,ZM,XXXXX
The jrxml file:
<?xml version="1.0" encoding="UTF-8"?>
<jasperReport xmlns="http://jasperreports.sourceforge.net/jasperreports" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://jasperreports.sourceforge.net/jasperreports http://jasperreports.sourceforge.net/xsd/jasperreport.xsd" name="exclude_band_for_csv" language="groovy" pageWidth="595" pageHeight="120" columnWidth="555" leftMargin="20" rightMargin="20" topMargin="0" bottomMargin="0" uuid="daaa60dc-b91b-4e9b-bbc0-6189af985ef9">
<property name="net.sf.jasperreports.export.csv.exclude.origin.band.1" value="pageHeader"/>
<property name="net.sf.jasperreports.export.csv.exclude.origin.band.2" value="pageFooter"/>
<queryString>
<![CDATA[]]>
</queryString>
<field name="Name" class="java.lang.String"/>
<field name="Address" class="java.lang.String"/>
<field name="Hobby" class="java.lang.String"/>
<pageHeader>
<band height="35" splitType="Stretch">
<staticText>
<reportElement uuid="9da294e6-b5b7-489f-9469-7edb539315da" x="117" y="0" width="380" height="20"/>
<textElement textAlignment="Center" verticalAlignment="Middle">
<font size="14"/>
</textElement>
<text><![CDATA[Page Header]]></text>
</staticText>
</band>
</pageHeader>
<detail>
<band height="20" splitType="Stretch">
<textField>
<reportElement uuid="6a615d39-86f1-4a74-8ae7-4f8ca8e19afe" x="0" y="0" width="100" height="20"/>
<textElement/>
<textFieldExpression><![CDATA[$F{Name}]]></textFieldExpression>
</textField>
<textField>
<reportElement uuid="df0929d2-34c0-4561-ab98-e6e5ce37fd11" x="100" y="0" width="100" height="20"/>
<textElement/>
<textFieldExpression><![CDATA[$F{Address}]]></textFieldExpression>
</textField>
<textField>
<reportElement uuid="675381d8-57b3-427f-88e4-ec4725ea3462" x="200" y="0" width="100" height="20"/>
<textElement/>
<textFieldExpression><![CDATA[$F{Hobby}]]></textFieldExpression>
</textField>
</band>
</detail>
<pageFooter>
<band height="45" splitType="Stretch">
<staticText>
<reportElement uuid="9da294e6-b5b7-489f-9469-7edb539315da" x="127" y="10" width="380" height="20"/>
<textElement textAlignment="Center" verticalAlignment="Middle">
<font size="14"/>
</textElement>
<text><![CDATA[Page Footer]]></text>
</staticText>
</band>
</pageFooter>
</jasperReport>
The report's design in iReport:
The result of JRPdfExporter will be:
Both bands are present in PDF file
The result of JRCsvExporter will be (the output csv file):
AAA,US,XXXXX
BBB,UK,XXXXX
CCC,ID,XXXXX
DDD,CC,XXXXX
EEE,SA,XXXXX
FFF,ZM,XXXXX
Both bands are absent in CSV file.
As you can see I've excluded two bands (Page Header and Page Footer) only for JRCsvExporter.
For more details you can also see this post: JasperReports: hide textfield when not HTML view